/usr/share/perl5/RG/Utils/Copf.pm is in librg-utils-perl 1.0.43-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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=head1 NAME
RG::Utils::Copf - Rost Lab perl utilities
=head1 SYNOPSIS
use RG::Utils::Copf;
=head1 FUNCTIONS
See module source for description.
=over
=item amino_acid_convert_3_to_1
=item amino_acid_convert_3_to_1_ini
=item brIniErr
=item brIniGetArg
=item brIniHelp
=item brIniHelpLoop
=item brIniHelpRdItself
=item brIniRdDef
=item brIniSet
=item brIniWrt
=item bynumber
=item bynumber_high2low
=item cleanUp
=item complete_dir
=item completeDir
=item convAliGen
=item convDsspGen
=item convFastamul2many
=item convFssp2Daf
=item convFsspGen
=item convGcg2fasta
=item convHssp2seq
=item convHsspGen
=item convMsf2saf
=item convPdb2seq
=item convPdbGen
=item convPhd2dssp
=item convPhd2seq
=item convPhdGen
=item convPir2fasta
=item convPirmulGen
=item convSaf2many
=item convSeq2fastaPerl
=item convSeq2seq
=item convSeq2seqOld
=item convSeqGen
=item convSwiss2fasta
=item copf
=item dsspGetChain
=item dsspRdSeq
=item dsspWrtFromPhd
=item errSbr
=item errSbrMsg
=item fastaRdGuide
=item fastaRdMul
=item fastaWrt
=item fastaWrtMul
=item fctRunTimeLeft
=item fctSeconds2time
=item gcgRd
=item gcgWrt
=item getDistanceNewCurveIde
=item getFileFormatQuick
=item get_in_keyboard
=item get_range
=item get_rangeHyphen
=item getSysARCH
=item hsspCorrectNali
=item hsspGetChain
=item hsspGetChainLength
=item hsspRdAli
=item hsspRdHeader
=item hsspRdSeqSecAccOneLine
=item ini
=item iniDef
=item iniHelpLoc
=item is_chain
=item isDaf
=item is_dssp
=item isFasta
=item isFastaMul
=item is_fssp
=item isGcg
=item is_hssp
=item isMsf
=item isPdb
=item is_pdbid
=item isPhdAcc
=item isPhdBoth
=item isPhdHtm
=item isPhdSec
=item isPir
=item isPirMul
=item is_ppcol
=item isRdb
=item is_rdb_htmref
=item is_rdb_htmtop
=item is_rdb_nnDb
=item isSaf
=item is_strip
=item isSwiss
=item msfBlowUp
=item msfCheckFormat
=item msfCompress
=item msfCountNali
=item msfRd
=item msfShorten
=item msfWrt
=item open_file
=item pdbExtrSequence
=item pirRdMul
=item pirWrtMul
=item pirWrtOne
=item rdRdbAssociative
=item rdRdbAssociativeNum
=item safCompress
=item safRd
=item safWrt
=item seqGenWrt
=item swissRdSeq
=item sysDate
=item sysGetUserLoc
=item sysRunProg
=item wrtLoc
=back
=head1 VARIABLES
=over
=back
=head1 AUTHOR
B. Rost <rost@rostlab.org>
L. Kajan <lkajan@rostlab.org>
=head1 SEE ALSO
=over
=item Main website
L<http://rostlab.org/>
=back
=cut
package RG::Utils::Copf;
use Carp qw| cluck :DEFAULT |;
use File::Temp;
no warnings 'deprecated';
#------------------------------------------------------------------------------#
# Copyright 1998 #
# Burkhard Rost rost@EMBL-Heidelberg.DE #
# Wilckensstr. 15 http://www.embl-heidelberg.de/~rost/ #
# D-69120 Heidelberg #
# version 0.1 May, 1998 #
#------------------------------------------------------------------------------#
INIT: {
#======================================================================
# Read environment parameters
#======================================================================
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
$scrName=$0; $scrName=~s/^.*\/|\.pl//g;
$scrGoal= "copff: converts protein file formats";
$scrIn= "toConvert toConvTo|files* format-out"; #
$scrNarg= 2; # minimal number of input arguments
# additional information about script
$okFormOut= "hssp,dssp,msf,saf,daf,fastamul,pirmul,fasta,pir,gcg";
$okFormIn= "hssp,dssp,fssp,msf,saf,fastamul,pirmul,fasta,pir,gcg,phdrdb,swiss,pdb";
@okFormOut=split(/,/,$okFormOut);@okFormIn=split(/,/,$okFormIn);
$okFormOutOr=join('|',@okFormOut);$okFormInOr=join('|',@okFormIn);
$scrHelpTxt= "Formats supported: \n";
$scrHelpTxt.=" * Input: ". $okFormOut."\n";
$scrHelpTxt.=" * Output: ". $okFormIn ."\n";
$scrHelpTxt.=" \n";
$scrHelpTxt.="Several ways to run the script:\n";
$scrHelpTxt.="in: 'file.msf file.hssp' -> convert MSF to HSSP (assigned according to extensions)\n"; #
$scrHelpTxt.="in: '*.msf hssp' -> all input MSF files converted to HSSP\n";
$scrHelpTxt.="in: 'file.listx hssp list'-> all files listed in 'file.list' converted to HSSP\n";
$scrHelpTxt.=" NOTE: the keyword 'list' makes things easier for me...\n";
$scrHelpTxt.=" if file named *.list, list is assumed!!\n";
$scrHelpTxt.="in: '*.f fastamul' -> many FASTAs converted to one big FASTAmul (e.g. database)\n";
$scrHelpTxt.="in: '' -> \n";
$scrHelpTxt.=" \n";
$scrHelpTxt.="Note 1: if your alignment format is none of the above, I suggest you convert it to\n";
$scrHelpTxt.=" the SAF format (see 'help saf' and 'help saf-syn'), which is the simplest.\n";
$scrHelpTxt.=" \n";
$scrHelpTxt.="Note 2: Sorry for inconveniences, writing this 'shit' was boring and time consuming\n";
$scrHelpTxt.=" -> for many conversions A -> B you will have to run the program repetively:\n";
$scrHelpTxt.=" A -> A1 , A1 -> A2, A2 -> B ...\n";
$scrHelpTxt.=" \n";
$scrHelpTxt.="Further options may be obtained by 'help FORMAT' ...\n";
$scrHelpTxt.=" \n";
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
}
#===============================================================================
sub copf {
$[ =1 ;
#-------------------------------------------------------------------------------
# copf package version of script
#-------------------------------------------------------------------------------
$[ =1 ; # sets array count to start at 1, not at 0
@PARAMS=@_; # pass from calling
($Lok,$msg)= &ini(); # initialise variables
if (! $Lok){ Carp::confess("--> ERROR during initialising $scrName \nmsg=$msg"); }
#-------------------------------------------------------------------------------
# do the job (here we go)
#-------------------------------------------------------------------------------
# general assignments to reduce typing
$formIn= $par{"formatIn"}; $extIn= $par{"ext_$formIn"};
$formOut=$par{"formatOut"}; $extOut=$par{"ext_$formOut"};
$fh="STDOUT" if ($Lverb);
$fh=$fhTrace if (! $Lverb);
$nfileIn=$#fileIn;
$itFile=0;
# --------------------------------------------------
# alignments
# --------------------------------------------------
# ------------------------------
if ($formIn eq "hssp"){ # in: HSSP
while (@fileIn) {
++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
next if (! $par{"doAgain"} && -e $fileOutDef);
&wrtLoc($fh) if ($par{"verbose"});
($Lok,$msg)=
&convHsspGen($fileIn,$chainIn[$itFile],$fileOutDef,$formOut,$extOut,
$par{"exeConvertSeq"},$par{"exeConvHssp2saf"},
$par{"doExpand"},$par{"frag"},$par{"extr"},
$par{"fileOutScreen"},$par{"dirWork"},$fhTrace,$par{"doSplitChain"});
print $fh "*** ERROR $scrName after convHsspGen\n","*** $msg\n" if (! $Lok || $Lok==2);}}
# ------------------------------
elsif ($formIn eq "fssp"){ # in: FSSP
while (@fileIn) {
++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
next if (! $par{"doAgain"} && -e $fileOutDef);
&wrtLoc($fh) if ($par{"verbose"});
($Lok,$msg)=
&convFsspGen($fileIn,$fileOutDef,$formOut,$extOut,$par{"exeFssp2daf"},
$par{"fileInclProt"},$par{"dirDssp"},$par{"dirWork"},$fhTrace);
print $fh "*** ERROR $scrName after convFsspGen\n","*** $msg\n" if (! $Lok || $Lok==2);}}
# ------------------------------
# in: MSF|SAF|FASTAmul
elsif ($formIn eq "msf" || $formIn eq "saf" ||
$formIn eq "fastamul" || $formIn eq "pirmul"){
while (@fileIn) {
++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
next if (! $par{"doAgain"} && -e $fileOutDef);
&wrtLoc($fh) if ($par{"verbose"});
($Lok,$msg)=
&convAliGen($fileIn,$fileOutDef,$formIn,$formOut,$extOut,
$par{"exeConvertSeq"},$par{"fileMatGcg"},$par{"doCompress"},
$par{"frag"},$par{"extr"},$par{"fileOutScreen"},$par{"dirWork"},$fhTrace);
print $fh "*** ERROR $scrName after convAliGen\n","*** $msg\n" if (! $Lok || $Lok==2);}
}
# change br 99-03 : commented out, since included in previous!
# # ------------------------------
# elsif ($formIn eq "pirmul"){ # in: PIRMUL
# while (@fileIn) {
# ++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
# next if (! $par{"doAgain"} && -e $fileOutDef);
# &wrtLoc($fh) if ($par{"verbose"});
# ($Lok,$msg)=
# &convPirmulGen($fileIn,$fileOutDef,$formOut,$extOut,
# $par{"frag"},$par{"extr"},$par{"dirWork"},$fhTrace);
# print $fh "*** ERROR $scrName after convPirmulGen\n","*** $msg\n" if (! $Lok || $Lok==2);}}
# --------------------------------------------------
# sequences
# --------------------------------------------------
# ------------------------------
# in: FASTA, SWISS, PIR, GCG
elsif ($formIn eq "fasta" || $formIn eq "swiss" || $formIn eq "pir" || $formIn eq "gcg"){
while (@fileIn) {
++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
next if (! $par{"doAgain"} && -e $fileOutDef);
&wrtLoc($fh) if ($par{"verbose"});
# out: ali
if ($formOut eq "hssp"){
($Lok,$msg)=
&convAliGen($fileIn,$fileOutDef,$formIn,$formOut,$extOut,
$par{"exeConvertSeq"},$par{"fileMatGcg"},$par{"doCompress"},
$par{"frag"},$par{"extr"},$par{"fileOutScreen"},$par{"dirWork"},$fhTrace);
print $fh "*** ERROR $scrName after convAliGen\n","*** $msg\n" if (! $Lok || $Lok==2); }
# out: sequence
else {
($Lok,$msg)=
&convSeqGen($fileIn,$fileOutDef,$formIn,$formOut,$extOut,
$par{"exeConvertSeq"},$par{"frag"},$par{"fileOutScreen"},
$par{"dirWork"},$fhTrace);
print $fh "*** ERROR $scrName after convSeqGen\n","*** $msg\n" if (! $Lok || $Lok==2);}}}
# ------------------------------
# in: PDB
elsif ($formIn eq "pdb"){
if ($formOut !~ /^(fasta|pir|gcg)/){
print $fh "*** ERROR $scrName supported only PDB -> FASTA|PIR|GCG\n";
Carp::confess("*** ERROR $scrName supported only PDB -> FASTA|PIR|GCG");}
while (@fileIn) {
++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
next if (! $par{"doAgain"} && -e $fileOutDef);
$chainIn=0;
$chainIn=shift @chainIn if (@chainIn);
&wrtLoc($fh) if ($par{"verbose"});
($Lok,$msg)=
&convPdbGen($fileIn,$chainIn,$fileOutDef,$formOut,$extOut,
$par{"exeConvertSeq"},$par{"frag"},$par{"dirWork"},$fhTrace);
print $fh "*** ERROR $scrName after convPdbGen\n","*** $msg\n" if (! $Lok || $Lok==2);}}
# ------------------------------
elsif ($formIn eq "dssp"){ # in: DSSP
if ($formOut !~ /^(fasta|pir|saf|msf|hssp)/){ #
print $fh "*** ERROR $scrName supported only DSSP -> FASTA|PIR|MSF|SAF2\n";
Carp::confess("*** ERROR $scrName supported only DSSP -> FASTA|PIR|MSF|SAF2");}
while (@fileIn) {
++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
next if (! $par{"doAgain"} && -e $fileOutDef);
$chainIn=0;
$chainIn=shift @chainIn if (@chainIn);
&wrtLoc($fh) if ($par{"verbose"});
($Lok,$msg)=
&convDsspGen($fileIn,$chainIn,$fileOutDef,$formOut,$extOut,
$par{"exeConvertSeq"},$par{"fileMatGcg"},
$par{"frag"},$par{"fileOutScreen"},$par{"dirWork"},$fhTrace,
$par{"doSplitChain"});
print $fh "*** ERROR $scrName after convDsspGen\n","*** $msg\n" if (! $Lok || $Lok==2);}}
# --------------------------------------------------
# PHD predictions
# --------------------------------------------------
# ------------------------------
# in: PHDrdb
elsif ($formIn =~ /^phdrdb/) {
while (@fileIn) {
++$itFile; $fileIn=shift @fileIn; $fileOutDef=shift @fileOutDef;
next if (! $par{"doAgain"} && -e $fileOutDef);
$chainIn=0;
$chainIn=shift @chainIn if (@chainIn);
&wrtLoc($fh) if ($par{"verbose"});
# out: msf
if ($formOut =~ /^(saf|msf)$/) {
print $fh "*** option PHD -> $formOut not implemented, yet!\n";
Carp::confess("*** option PHD -> $formOut not implemented, yet!"); }
# out: DSSP, nicer, HTML, ..
else {
($Lok,$msg)=
&convPhdGen($fileIn,$chainIn,$fileOutDef,$formIn,$formOut,$extOut,
$par{"frag"},$par{"fileOutScreen"},$par{"dirWork"},$fhTrace);
print $fh "*** ERROR $scrName after convPhdGen\n","*** $msg\n" if (! $Lok || $Lok==2);
}}}
# **************************************************
# unrecognised input format
# **************************************************
else {
Carp::confess("*** ERROR $scrName input format $formIn not supported");}
#-------------------------------------------------------------------------------
# work done, go home
#-------------------------------------------------------------------------------
# ------------------------------
# deleting intermediate files
&cleanUp() if (! $par{"debug"});
# ------------------------------
# final words
if ($Lverb) { $timeEnd=time; # runtime , run time
$timeRun=$timeEnd-$timeBeg;
if( $par{debug} ){ cluck
"--- $scrName ended on $Date (run time=".&fctSeconds2time($timeRun).")"; }
# ------------------------------
# output files
if( $par{debug} )
{
if ($#fileOut==1){
printf STDERR "--- %-20s %-s\n","output file:",$fileOut[1];}
elsif ($#fileOut > 10){
printf STDERR "--- %-20s %-s\n","output files:","";
foreach $file (@fileOut){
print STDERR "$file," if (-e $file);}
print STDERR "\n"; }
elsif ($#fileOut > 0){
print STDERR "--- output files:";
foreach $_(@fileOut){
printf STDERR "--- %-20s %-s\n"," ",$_ if (-e $_);}}
}
}
return(1,"ok $sbrName");
} # end of copf
#===============================================================================
sub ini {
$[ =1 ;
#-------------------------------------------------------------------------------
# initialises variables/arguments
#-------------------------------------------------------------------------------
$sbrName="$scrName".":ini";
# ------------------------------
foreach $arg(@PARAMS){ # highest priority arguments
next if ($arg !~/=/);
if ($arg=~/dirLib=(.*)$/) { $dir= $1;}
elsif ($arg=~/dirHome=(.*)$/i) { $par{"dirHome"}= $1;}
elsif ($arg=~/ARCH=(.*)$/) { $ARCH= $1;}
elsif ($arg=~/PWD=(.*)$/) { $PWD= $1;}
elsif ($arg=~/^packName=(.*)/) { $par{"packName"}=$1;
shift @PARAMS if ($PARAMS[1] eq $arg); } }
# ******************************
# ERROR
return(&errSbrMsg("after $0:",
"missing dirHome, please add the command line option:\n".
"dirHome=THE_PATH_WHERE_THIS_SCRIPT_SITS",$SBR))
if( !$par{dirHome} || !-e $par{dirHome} );
# ------------------------------
# get architecture $ARCH=
$ARCH=$ARCH || &getSysARCH();
$PWD= $ENV{'PWD'} if (! defined $PWD && defined $ENV{'PWD'});
$PWD=~s/\/$// if (defined $PWD && $PWD=~/\/$/);
$pwd= $PWD if (defined $PWD);
$pwd.="/" if (defined $pwd && $pwd !~ /\/$/);
# ------------------------------
$timeBeg= time; # date and time
$Date= &sysDate();
# ------------------------------
# first settings for parameters
&iniDef(); # NOTE: may be overwritten by DEFAULT file!!!!
# ------------------------------
# HELP stuff
&iniHelpLoc();
($Lok,$msg)= # want help?
&brIniHelpLoop($scrName,%tmp);
return(&errSbrMsg("after lib-ut:brIniHelpLoop",$msg,$SBR)) if (! $Lok);
exit if ($msg eq "fin");
# ------------------------------
# read command line input
$#fileIn=0;
@argUnk= # standard command line handler
&brIniGetArg();
$LuseBigConvertSeq=0;
foreach $arg (@argUnk){ # interpret specific command line arguments
next if ($arg=~/^(dirLib|ARCH|PWD|packName)=/);
if ($arg=~/^verb\w*2/) {$par{"verb2"}=$Lverb2= 1;}
elsif ($arg=~/^verbose/) {$par{"verbose"}=$Lverb= 1;}
elsif ($arg=~/not_?([vV]er|[sS]creen)/ ) {$par{"verbose"}=$Lverb= 0; }
elsif ($arg=~/^expand$/i) {$par{"doExpand"}= 1;}
elsif ($arg=~/^compress$/i) {$par{"doCompress"}= 1;}
elsif ($arg=~/^nocompr?e?s?s?$/i) {$par{"doCompress"}= 0;}
elsif ($arg=~/^list$/i) {$par{"isList"}= 1;}
elsif ($arg=~/^skip$/i) {$par{"doAgain"}= 0;}
elsif ($arg=~/^big$/i) {$LuseBigConvertSeq= 1;}
elsif ($arg=~/^split$/i) {$par{"doSplitChain"}= 1;}
elsif ($arg=~/^de?bu?g$/i) {$par{"debug"}= 1;}
elsif ($arg =~/^formatIn=(.*)$/) {$par{"formatIn"}=$formIn=$1;}
elsif ($arg =~/^formatOut=(.*)$/) {$par{"formatOut"}=$formOut=$1;}
elsif ($arg=~/^(hssp|msf|dssp|fssp|saf|daf|fastamul|pirmul|swiss|fasta|pir|gcg)$/i){
$par{"formatOut"}=$1; $par{"formatOut"}=~tr/[A-Z]/[a-z]/;}
elsif ($arg=~/^fileOut=(.+)$/) {$par{"fileOut"}=$fileOut=$1;}
# process chains (PDB)
elsif ($arg=~/^(.*)($par{"ext_pdb"}|\.brk)\_([A-Z0-9])/){
return(0,"*** ERROR $sbrName: kwd=$arg not correct syntax (use:file.pdb_C)\n")
if (! defined $1 || ! -e $1);
next if (length($1)<2 || ! -e $1);
push(@fileIn,$1);push(@chainIn,$2);}
# process chains (dssp)
elsif ($arg=~/^(.*$par{"ext_dssp"})\_([A-Z0-9])/){
return(0,"*** ERROR $sbrName: kwd=$arg not correct syntax (use:file.dssp_C)\n")
if (! defined $1 || ! -e $1);
next if (length($1)<2 || ! -e $1);
push(@fileIn,$1);push(@chainIn,$2);}
# process chains (hssp)
elsif ($arg=~/^(.*$par{"ext_hssp"})\_([A-Z0-9])/){
return(0,"*** ERROR $sbrName: kwd=$arg not correct syntax (use:file.hssp_C)\n")
if (! defined $1 || ! -e $1);
next if (length($1)<2 || ! -e $1);
push(@fileIn,$1);push(@chainIn,$2);}
elsif ($arg eq $PARAMS[2]){ # to enable calling by 'copf 1ppt.hssp 1ppt.daf'
next;}
elsif ($arg=~/^expand$/i) {$par{"doExpand"}= 1;}
else {
return(0,"*** ERROR $sbrName: '$arg' file does not exist or kwd not understood\n");}}
# ------------------------------
# replace binary
# if ($LuseBigConvertSeq){
# $par{"exeConvertSeq"}=$par{"exeConvertSeqBig"};
# if (! -e $par{"exeConvertSeq"} && ! -l $par{"exeConvertSeq"}){
# print
# "*** you want the BIG for convert_seq.$ARCH(".
# $par{"exeConvertSeq"}."), however none there!\n";
# exit;}}
# ------------------------------
# output file given?
$fileOut=$par{"fileOut"} if (defined $par{"fileOut"} && $par{"fileOut"} &&
$par{"fileOut"} ne "unk");
# ------------------------------
# correct blabla levels
$par{"verbose"}=$par{"verb2"}=1 if ($par{"debug"});
# ------------------------------
# require packages
# ------------------------------
# foreach $exe ("exeConvHssp2saf","exeFssp2daf") {
# next if ($par{"$exe"}=~/\.pl/);
# if (! -e $par{"$exe"}){
# print "*** WARN or ERROR (?) $scrName: failed to find package ",$par{"$exe"},"\n";
# next; }
# $Lok= require $par{"$exe"};
# Carp::confess("*** $scrName: failed to require perl package '".$par{"$exe"}."'\n") if (! $Lok);}
# --------------------------------------------------
# digest input file formats
# --------------------------------------------------
return(0,"*** ERROR $sbrName: no input file given!!\n") if ($#fileIn==0);
# any file ending with 'list'?
foreach $fileIn (@fileIn){
if ($fileIn =~ /\.list/) {
$par{"isList"}=1;
last;}}
if (defined $par{"isList"} && $par{"isList"} eq "1"){ # input is file list
&open_file("$fhin","$fileIn[1]") ||
return(0,"*** ERROR $sbrName: failed to open fileIn=$fileIn\n");
$#fileIn=$#chainIn=$#dir=0;
while (<$fhin>) {
$_=~s/\s|\n//g;$file=$_;
# for DSSP and HSSP: digest chains
if ($file =~ /^(.*)($par{"ext_hssp"}|$par{"ext_dssp"})\_([A-Z0-9])$/){
$file=$1.$2;$chain=$3;}
else {$chain="*";}
# add dir if file not existing (hssp)
if (! -e $file && $file =~ /^.*$par{"ext_hssp"}/){
if (! $#dir){@tmp=split(/,/,$par{"dirHssp"});
foreach $tmp(@tmp){
push(@dir,&complete_dir($tmp)) if (-d $tmp);}}
foreach $dir (@dir){ $tmp=$dir.$file;
if (-e $tmp){$file=$tmp;
last;}}}
# add dir if file not existing (dssp)
elsif (! -e $file && $file =~ /^.*$par{"ext_dssp"}/){
if (! $#dir){@tmp=split(/,/,$par{"dirDssp"});
foreach $tmp(@tmp){
push(@dir,&complete_dir($tmp)) if (-d $tmp);}}
foreach $dir (@dir){ $tmp=$dir.$file;
if (-e $tmp){$file=$tmp;
last;}}}
if (! -e $file){ print
"-*- WARN $sbrName no file=$file, (ignored)\n" if ($par{"verbose"});
next;}
push(@fileIn,$file);push(@chainIn,$chain);}close($fhin);}
# --------------------------------------------------
# watch chain if not provided in list!
else {
foreach $it (1..$#fileIn){
$chainIn[$it]="*" if (! defined $chainIn[$it]);}}
# ------------------------------
# determine input format
if( !$par{formatIn} )
{
($Lok,$msg) = &getFileFormatQuick($fileIn[1]);
if (! $Lok || $msg =~ /ERROR/ || length($msg)>10 || length($msg)<3)
{
return(0,"*** ERROR $sbrName: could not determine format for file list ($fileIn[1])\n");
}
$par{"formatIn"}=$msg;
if( $par{debug} ){ cluck("guessed file format of '$fileIn[1]': $par{formatIn}"); }
}
$par{"formatIn"}=~tr/[A-Z]/[a-z]/;
# case FSSP : you must have DSSP directory
if ($par{"formatIn"} eq "fssp"){
@tmp=split(/,/,$par{"dirDssp"});$Lok=0;
foreach $dir (@tmp){
if (-d $dir){$Lok=1;$par{"dirDssp"}=$dir;$par{"dirDssp"}.="/" if ($dir !~/\/$/);
last;}}
return(0,"*** ERROR $sbrName: for FSSP you must provide the directory for the DSSP\n".
"*** database by the argument 'dirDssp=/home/data/dssp'\n")
if (!$Lok);}
# ------------------------------
# input format supported?
if ($par{"formatIn"} !~ /^($okFormInOr)$/ && $par{"formatIn"} !~ /^phdrdb/i )
{
my $msg = "*** ERROR $sbrName: input format '".$par{"formatIn"}."' (of files in $fileIn[1]) unsupported\n";
cluck( $msg );
return(0,$msg);
}
# ------------------------------
$#tmpx=0; # security: allow only files with same format as first
foreach $file (@fileIn[2..$#fileIn]){
($Lok,$msg)=&getFileFormatQuick($file);
next if ($msg !~/$par{"formatIn"}/i);
next if (! defined $file);
push(@tmpx,$file);}
@fileIn=($fileIn[1],@tmpx);
# ------------------------------
# determine output format
# (1) not provided, but 2nd arg = file.WANTED_CONVERSION
if (! defined $par{"formatOut"} || length($par{"formatOut"})<2 || $par{"formatOut"} eq "unk"){
$fileOut=$PARAMS[2];
$par{"formatOut"}=$fileOut; $par{"formatOut"}=~s/^.*\.([^\.]+)$/$1/;
$par{"formatOut"}=~tr/[A-Z]/[a-z]/;}
# ------------------------------
# output format supported?
return(0,"*** ERROR $sbrName: output format '".$par{"formatOut"}."' unsupported\n")
if ($par{"formatOut"} !~ /^($okFormOutOr)$/);
# ------------------------------
# final settings
$Lok= # standard settings
&brIniSet(); return(0,"*** ERROR $sbrName: after lib-ut:brIniSet\n") if (! $Lok);
$#fileOut=0; # reset output files
$#fileOutDef=0; # standard output names
# note: for single input file: name already assigned
if (! defined $fileOut){
$ct=0;
foreach $fileIn (@fileIn){
$formIn= $par{"formatIn"};
# special for Brookhaven:
if ($formIn eq "pdb" && $fileIn =~/\.brk/) {
$extIn=".brk";}
else {
$extIn= $par{"ext_$formIn"};}
$formOut=$par{"formatOut"}; $extOut=$par{"ext_$formOut"};
$extOut= $par{"ext_dsspPhd"} if ($formIn=~/phdrdb/ && $formOut=~/^dssp/);
$fileOut=$fileIn;
# purge dir
$fileOut=~s/^.*\///g;
# replace extension
$fileOut=~s/(\.f(asta)?(mul)?|\.pirmul|$extIn(_.)?)$/$extOut/i;
# add dirOut
$fileOut=$par{"dirOut"}.$fileOut;
++$ct;
$fileOut=~s/$extOut$/$par{"ext_chain"}$chainIn[$ct]$extOut/
if ($formIn =~/[hd]ssp/ && defined $chainIn[$ct] && $chainIn[$ct] =~/[A-Z0-9]/);
# security
$fileOut.=".tmp" if ($fileOut eq $fileIn);
push(@fileOutDef,$fileOut);}}
else{
$formOut=$par{"formatOut"};
# security
$fileOut.=".tmp" if (defined $fileIn && $fileOut eq $fileIn);
push(@fileOutDef,$fileOut);}
# correction for single: add file name
$par{"fileOut"}=$fileOut if ($#fileOutDef==1 && $par{"fileOut"} !~ $par{"ext_".$formOut});
# correct settings for executables: add directories
if (0){
foreach $kwd (keys %par){
next if ($kwd !~/^exe/);
next if (-e $par{$kwd} || -l $par{$kwd});
}
}
# ------------------------------
# check errors
$exclude=
"exeFssp2daf,exeConvHssp2saf,exeConvertSeqBig"; # yy to exclude from error check
($Lok,$msg)= #
&brIniErr($exclude); return(0,"*** ERROR $sbrName: after lib-ut:brIniErr\n".$msg) if (! $Lok);
# yy
# yy add syntax check
# yy
# ------------------------------
# massage temporary files
if( $par{"dirWork"} && $par{"dirWork"} ne "unk" && length($par{"dirWork"}) > 0) {
$par{"fileOutTrace"}= $par{"dirWork"}.$par{"fileOutTrace"}
if ($par{"fileOutTrace"} !~ /$par{"dirWork"}/ &&
defined $par{"fileOutTrace"} &&
$par{"fileOutTrace"} ne "unk" && length($par{"fileOutTrace"}) > 0);
$par{"fileOutScreen"}=$par{"dirWork"}.$par{"fileOutScreen"}
if ($par{"fileOutScreen"} !~ /$par{"dirWork"}/ &&
defined $par{"fileOutScreen"} &&
$par{"fileOutScreen"} ne "unk" && length($par{"fileOutScreen"}) > 0);
}
# --------------------------------------------------
# trace file
# --------------------------------------------------
if( $par{"fileOutTrace"} && $par{"fileOutTrace"} ne "unk" &&
length($par{"fileOutTrace"}) > 0) {
print "--- \t open $fhTrace for trace file ",$par{"fileOutTrace"}," \n" if ($Lverb2);
&open_file("$fhTrace",">$par{fileOutTrace}") ||
return(&errSbr("failed to open new file for trace : ".$par{"fileOutTrace"},$SBR));}
else {
$fhTrace="STDOUT";}
$fhTrace="STDOUT" if ($par{"debug"});
# ------------------------------
# write settings
# ------------------------------
if ($par{"verb2"}){
$exclude="kwd,dir*,ext*"; # keyword not to write
$fhloc="STDOUT";
$fhloc=$fhTrace if (! $par{"debug"});
($Lok,$msg)=
&brIniWrt($exclude,$fhloc);
return(&errSbrMsg("after lib-ut:brIniWrt",$msg,$SBR)) if (! $Lok); }
# ------------------------------
undef %tmp; # clean memory
return(1,"ok $sbrName");
} # end of ini
#===============================================================================
sub iniDef {
$[ =1 ;
#-------------------------------------------------------------------------------
# iniDef initialise defaults
#-------------------------------------------------------------------------------
# d.d
# --------------------
# directories
# <<<<<<<<<<<<<<<<<<<<
# normal
$par{"dirSrc"}= $par{"dirHome"}. "/lib/"; # all source except for binaries
$par{"dirSrcMat"}= $par{"dirSrc"}. "mat/"; # general material
# perl libraries
$par{"dirPerl"}= $par{"dirSrc"}. "perl/" if (! defined $par{"dirPerl"});
$par{"dirPerlScr"}= $par{"dirPerl"}. "scr/"; # perl scripts needed
$par{"dirBin"}= $par{"dirHome"}. "/bin/"; # FORTRAN binaries of programs needed
# lkajan: there's got to be a better way to do this
# if ($0=~/maxhom/){
# $par{"dirSrc"}= $par{"dirHome"}. "scr/"; # all source except for binaries
# $par{"dirSrcMat"}= $par{"dirHome"}. "mat/"; # general material
# $par{"dirPerl"}= $par{"dirHome"}. "scr/" if (! defined $par{"dirPerl"});
# $par{"dirPerlScr"}= $par{"dirHome"}. "scr/"; # perl scripts needed
# }
# <<<<<<<<<<<<<<<<<<<<
# for porting PHD asf
# lkajan: there's got to be a better way to do this
# if( $0=~/phd/ ){
# $par{"dirSrcMat"}= "/nfs/home1/yachdav/work/SNAP/phd/". "mat/"; # general material
# $par{"dirPerl"}= "/nfs/home1/yachdav/work/SNAP/phd/". "scr/"; # perl libraries
# $par{"dirPerlScr"}= "/nfs/home1/yachdav/work/SNAP/phd/". "scr/"; # perl scripts needed
# $par{"dirBin"}= "/nfs/home1/yachdav/work/SNAP/phd/". "bin/"; # FORTRAN binaries of programs needed
# }
# elsif( $0=~/prof/ ){
$par{"dirSrcMat"}= "$par{dirHome}/mat/"; # general material
#$par{"dirPerl"}= "$par{dirHome}embl/scr/"; # perl libraries # lkajan: deprecated
#$par{"dirPerlScr"}= "$par{dirHome}embl/scr/"; # perl scripts needed # lkajan: wrong
$par{"dirBin"}= "/usr/bin/"; # FORTRAN binaries of programs needed
# }
$par{"dirPerlPack"}= $par{"dirPerlScr"}."pack/"; # perl scripts needed
$par{"dirConvertSeq"}= $par{"dirBin"};
$par{"dirOut"}= ""; # directory for output files
$par{"dirWork"}= ""; # working directory
# databases to search for files
$par{"dirHssp"}= "/home/rost/data/hssp/,/data/hssp/"; # dir for HSSP files
$par{"dirDssp"}= "/home/rost/data/dssp/,/data/dssp/"; # dir for DSSP files
$par{"dirFssp"}= "/home/rost/data/fssp/,/data/fssp/"; # dir for FSSP files
$par{"dirSwiss"}= "/home/rost/data/swissprot/current/,/data/swissprot/current/"; #
# dir for SWISS-PROT files
# additional user specified db
$par{"dirMsf"}= "unk"; # dir for MSF files
# additional user specified db
$par{"dirMsf"}= "unk"; # dir for MSF files
$par{"dirSaf"}= "unk"; # dir for SAF files
$par{"dirDaf"}= "unk"; # dir for DAF files
$par{"dirFastaMul"}= "unk"; # dir for FASTA files
$par{"dirPirMul"}= "unk"; # dir for PIR files
$par{"dirFasta"}= "unk";
$par{"dirGcg"}= "unk"; # dir for GCG files
# further on work
# --------------------
# files
$par{"title"}= "unk"; # output files will be called 'Pre-title.ext'
$par{"titleTmp"}= "COPF-tmp"."jobid"; # title used for temporary files
$par{"fileOut"}= "unk";
# lkajan: I see no reason to /set/ these by default
#$par{"fileOutTrace"}= "COPF-TRACE-"."jobid".".tmp"; # file tracing some warnings and errors
#$par{"fileOutScreen"}= "COPF-SCREEN-"."jobid".".tmp"; # file dumping the screen for convert_seq output
$par{"fileOutTrace"}= '';
$par{"fileOutScreen"}= '';
$par{"fileHelpMan"}= "unk"; # file with manual
$par{"fileHelpOpt"}= "unk"; # file with options
$par{"fileHelpHints"}= "unk"; # file with hints, note: also passed as par{scrHelpHints}
$par{"fileHelpProblems"}= "unk"; # file with known problems, also passed as par{scrHelpProblems}
# file extensions
# $par{"preOutTmp"}= "Out-";
# $par{"extOut"}= ".tmp";
$par{"ext_chain"}= "_"; # for extraction of chain, output file will contain 'ext_chain'.chain
$par{"ext_hssp"}= ".hssp";
$par{"ext_dssp"}= ".dssp";
$par{"ext_fssp"}= ".fssp";
$par{"ext_msf"}= ".msf";
$par{"ext_pdb"}= ".pdb";
$par{"ext_daf"}= ".daf";
$par{"ext_saf"}= ".saf";
$par{"ext_fasta"}= ".f";
$par{"ext_fastamul"}= ".fasta";
$par{"ext_pirmul"}= ".pir";
$par{"ext_pir"}= ".pir";
$par{"ext_fasta"}= ".f";
$par{"ext_swiss"}= ""; # no extension, simply following structure 'id_species'
$par{"ext_gcg"}= ".gcg";
$par{"ext_phdrdbboth"}= ".rdbPhd";
$par{"ext_dsspPhd"}= ".dsspPhd";
$par{"pre_id"}= 0; # additional information added to protein name,
# e.g. 'pre_id=hssp|1ppt'
# file handles
$fhin= "FHIN";
$fhTrace= "FHTRACE";
# --------------------
# job control
$par{"jobid"}= "jobid"; # unique job identifier (set to $$ if not defined)
$par{"debug"}= 0; # if 1 : keep (most) temporary files
$par{"verbose"}=$Lverb= 0; # blabla on screen
$par{"verb2"}=$Lverb2= 0; # more verbose blabla
# --------------------
# parameters
$par{"doHsspStrip"}= 0; # also write the HSSP strip file
$par{"doExpand"}= 0; # expand insertions in HSSP sequences?
$par{"doCompress"}= 1; # delete insertions in guide sequence for conversion to HSSP?
$par{"doSplitChain"}= 0; # split HSSP|DSSP|PDB files -> FASTA into chains
$par{"frag"}= 0; # convert fragments, only? Use the following notation:
# '1-55,77-99' to get two fragments one from 1-55, the other from 77-99
# NOTE: output files will be named xyz_1_55 and xyz_77_99
$par{"extr"}= 0; # extract particular protein from alignment format?
# provide the number of the protein in the alignment for which you want
# the sequence written into the output file
$par{"doAgain"}= 1; # if 1: existing files overwritten!
$par{"fileInclProt"}= 0; # contains ids to include, syntax PDBids + chain 1pdbC (or h|f|dssp files)
# note: used only for FSSP->DAF
# $par{"fileMatGcg"}= $par{"dirSrcMat"}. "Maxhom_GCG.metric"; # MAXHOM-GCG matrix
$par{"fileMatGcg"}= $par{"dirSrcMat"}. "Maxhom_McLachlan.metric"; # MAXHOM-GCG matrix
# $par{"fileMatGcg"}= $par{"dirSrcMat"}. "Maxhom_Blosum.metric"; # MAXHOM-GCG matrix
# needed for conversion into HSSP format!
# --------------------
# executables
$par{"exeConvertSeq"}= "$par{dirConvertSeq}convert_seq";
$par{"exeConvertSeqBig"}= "$par{dirConvertSeq}convert_seq";
# $par{"exeFssp2daf"}= $par{"dirPerlPack"}. "conv_fssp2daf_lh.pm";
$par{"exeFssp2daf"}= $par{"dirPerlScr"}. "conv_fssp2daf_lh.pl";
$par{"exeConvHssp2saf"}= $par{"dirPerlPack"}. "conv_hssp2saf.pm";
# $par{"exeConvHssp2saf"}= $par{"dirPerlScr"}. "conv_hssp2saf.pl";
} # end of iniDef
#===============================================================================
sub iniHelpLoc {
$[ =1 ;
#-------------------------------------------------------------------------------
# iniHelpLoc initialising some variables
#-------------------------------------------------------------------------------
# standard help
$tmp=0;
$tmp=$par{"packName"} if (defined $par{"packName"});
# lkajan: not entirely sure - sourceFile is supposed to be module or command name?
#if( ! $tmp ) { $tmp = __FILE__; }
$tmp=$0 if (! defined $tmp || ! $tmp);
$tmp=~s/^\.\/// if ($tmp=~/^\.\//);$tmpSource=$tmp;
%tmp=('sourceFile', $tmp, 'scrName',$scrName, 'scrIn',$scrIn, 'scrGoal', $scrGoal, 'scrNarg',$scrNarg,
'scrHelpTxt', $scrHelpTxt);
$tmp{"scrNameFull"}=$0;
# missing stuff
$tmp{"s_k_i_p"}= "problems,manual,hints";
# special help
$tmp{"scrAddHelp"}= "";
$tmp{"special"}= "expand,compress,nocompress,list,split,";
$tmp{"special"}= "skip,";
$tmp{"special"}.= "help saf-syn,";
$tmp{"special"}.= "big,";
$tmp{"expand"}= "OR doExpand=1, do expand HSSP deletions (conversion to MSF|SAF)";
$tmp{"compress"}= "OR doCompress=1, do delete insertions in MASTER (conversion to HSSP)";
$tmp{"nocompress"}= "OR doCompress=0, do NOT delete insertions in MASTER (conversion to HSSP)";
$tmp{"list"}= "OR isList=1, input file is list of files (extension *.list recognised!)";
$tmp{"split"}= "OR doSplitChain=1 split DSSP chains when converting to FASTA!";
$tmp{"skip"}= "OR doAgain=0, no action if output file existing!";
$tmp{"big"}= " use BIG binaries for *->hssp!";
undef %tmp2;
foreach $form (@okFormIn,@okFormOut){
next if (defined $tmp2{$form});$tmp2{$form}=1;$formTmp=$form;$formTmp=~tr/[a-z]/[A-Z]/;
$tmp{"special"}.= "help $form".",";
$tmp{"scrAddHelp"}.=
"help ".$form." " x (9-length($form)).": ".$formTmp." " x (10 -length($form))."format specific info\n";}
$tmp{"special"}=~s/,*$//g;
$tmp{"scrAddHelp"}.= "help saf-syn : specification of SAF format\n";
# $tmp{"scrAddHelp"}= "help zzz : all info on zzz format\n";
# ------------------------------
# alignment IN / OUT
$tmp{"help hssp"}= "DES: HSSP = Homology derived Secondary Structure of Proteins format (ali, IN | OUT)\n";
$tmp{"help hssp"}.= "OUT: MSF|DAF|SAF|FASTAmul|PIRmul|FASTA|PIR \n";
$tmp{"help hssp"}.= "OPT: The following options are available\n";
$tmp{"help hssp"}.= "OPT: \n";
$tmp{"help hssp"}.= "OPT: expand -> expand the deletion list when writing\n";
$tmp{"help hssp"}.= "OPT: * RESTRICT: for MSF and SAF output, only!!\n";
$tmp{"help hssp"}.= "OPT: extr=N -> extract sequence of protein N\n";
$tmp{"help hssp"}.= "OPT: * RESTRICT: for single sequence output, only!\n";
$tmp{"help hssp"}.= "OPT: default for HSSP->PIR/FASTA: extract guide seq (N=1)!\n";
$tmp{"help hssp"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help hssp"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help hssp"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help hssp"}.= "OPT: \n";
$tmp{"help hssp"}.= "OPT: chain=A,B -> selects only the chains A and B\n";
$tmp{"help hssp"}.= "OPT: NOTE: pass the identifier for chain C as \n";
$tmp{"help hssp"}.= "OPT: file.hssp_C\n";
$tmp{"help hssp"}.= "OPT: providing a chain disables the option 'frag=N-M'\n";
# $tmp{"help hssp"}.= "OPT: split -> split HSSP|DSSP|PDB files -> FASTA into chains\n";
$tmp{"help pdb"}= "DES: PDB\n";
$tmp{"help pdb"}.= "OUT: FASTAmul|FASTA|PIR|PIRmul|GCG \n";
$tmp{"help pdb"}.= "OPT: The following options are available\n";
$tmp{"help pdb"}.= "OPT: chain=A,B -> selects only the chains A and B\n";
$tmp{"help pdb"}.= "OPT: NOTE: pass the identifier for chain C as \n";
$tmp{"help pdb"}.= "OPT: file.pdb_C\n";
$tmp{"help pdb"}.= "OPT: providing a chain disables the option 'frag=N-M'\n";
$tmp{"help pdb"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help pdb"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help pdb"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
# $tmp{"help pdb"}.= "OPT: split -> split HSSP|DSSP|PDB files -> FASTA into chains\n";
$tmp{"help msf"}= "DES: MSF = Multiple Sequence Format (ali, IN | OUT)\n";
$tmp{"help msf"}.= "OUT: HSSP|SAF|FASTAmul|FASTA \n";
$tmp{"help msf"}.= "OPT: The following options are available\n";
$tmp{"help msf"}.= "OPT: compress -> delete insertions in GUIDE sequence\n";
$tmp{"help msf"}.= "OPT: * RESTRICT: for HSSP output, only!!\n";
$tmp{"help msf"}.= "OPT: extr=N -> extract sequence of protein N\n";
$tmp{"help msf"}.= "OPT: * RESTRICT: for single sequence output, only!\n";
$tmp{"help msf"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help msf"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help msf"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help saf"}= "DES: SAF = Simple Alignment Format (ali, IN | OUT)\n";
$tmp{"help saf"}.= "DES: resembles MSF, but less restrictive\n";
$tmp{"help saf"}.= "OUT: HSSP|MSF|FASTAmul|FASTA|PIRmul|PIR\n";
$tmp{"help saf"}.= "OPT: The following options are available\n";
$tmp{"help saf"}.= "OPT: compress -> delete insertions in GUIDE sequence\n";
$tmp{"help saf"}.= "OPT: * RESTRICT: for HSSP output, only!!\n";
$tmp{"help saf"}.= "OPT: extr=p1-p2,p3 -> extract sequence of proteins\n";
$tmp{"help saf"}.= "OPT: any list ok, e.g., '1-5,7,19-20,35'\n";
$tmp{"help saf"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help saf"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help saf"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help saf"}.= " \n";
$tmp{"help saf"}.= " To learn the detailed specifications about the SAF format , please typ:\n";
$tmp{"help saf"}.= "$tmpSource help saf-syn\n";
$tmp{"help saf"}.= " \n";
$tmp{"help saf-syn"}= "\n";
$tmp{"help saf-syn"}.= "============================================================\n";
$tmp{"help saf-syn"}.= "Specification of SAF (Simple Alignment Format)\n";
$tmp{"help saf-syn"}.= "============================================================\n";
$tmp{"help saf-syn"}.= "\n";
$tmp{"help saf-syn"}.= "NOTE: in principle SAF is like MSF ommitting the header, and\n";
$tmp{"help saf-syn"}.= " not requiring the MSF stringency.\n";
$tmp{"help saf-syn"}.= "NEW: Additional features are:\n";
$tmp{"help saf-syn"}.= " * comment lines can be inserted anywhere (by '#')\n";
$tmp{"help saf-syn"}.= " * unaligned regions do not have to be filled in\n";
$tmp{"help saf-syn"}.= "\n";
$tmp{"help saf-syn"}.= "------------------------------\n";
$tmp{"help saf-syn"}.= "EACH ROW\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= "two columns: 1. name (protein identifier, shorter than 15 characters)\n";
$tmp{"help saf-syn"}.= " 2. one-letter sequence (any number of characters)\n";
$tmp{"help saf-syn"}.= " insertions: dots (.), or hyphens (-)\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= "EACH BLOCK\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= "rows: 1. row must be guide sequence (i.e. always the same name,\n";
$tmp{"help saf-syn"}.= " this implies, in particular, that this sequence shold\n";
$tmp{"help saf-syn"}.= " not have blanks\n";
$tmp{"help saf-syn"}.= " 2, ..., n the aligned sequences\n";
$tmp{"help saf-syn"}.= " comments: * rows beginning with a '#' will be ignored\n";
$tmp{"help saf-syn"}.= " * rows containing only blanks, dots, numbers will also be ignored\n";
$tmp{"help saf-syn"}.= " (in particular numbering is possible)\n";
$tmp{"help saf-syn"}.= "\n";
$tmp{"help saf-syn"}.= "unspecified: * order of sequences 2-n can differ between the blocks,\n";
$tmp{"help saf-syn"}.= " * not all 2-n sequences have to occur in each block,\n";
$tmp{"help saf-syn"}.= " * \n";
$tmp{"help saf-syn"}.= " * BUT: whenever a sequence is present, it should have\n";
$tmp{"help saf-syn"}.= " * dots for insertions rather than blanks\n";
$tmp{"help saf-syn"}.= " * \n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= "NOTE\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= " The 'freedom' of this format has various consequences:\n";
$tmp{"help saf-syn"}.= " * identical names in different rows of the same block\n";
$tmp{"help saf-syn"}.= " are not identified. Instead, whenever this applies,\n";
$tmp{"help saf-syn"}.= " the second, (third, ..) sequences are ignored.\n";
$tmp{"help saf-syn"}.= " e.g. \n";
$tmp{"help saf-syn"}.= " t2_11751 EFQEDQENVN \n";
$tmp{"help saf-syn"}.= " name-1 ...EDQENvk\n";
$tmp{"help saf-syn"}.= " name-1 GGAPTLPETL\n";
$tmp{"help saf-syn"}.= " will be interpreted as:\n";
$tmp{"help saf-syn"}.= " t2_11751 EFQEDQENVN \n";
$tmp{"help saf-syn"}.= " name-1 ...EDQENvk\n";
$tmp{"help saf-syn"}.= " wheras:\n";
$tmp{"help saf-syn"}.= " t2_11751 EFQEDQENVN \n";
$tmp{"help saf-syn"}.= " name-1 ...EDQENvk\n";
$tmp{"help saf-syn"}.= " name_1 GGAPTLPETL\n";
$tmp{"help saf-syn"}.= " has three different names.\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= "EXAMPLE 1\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= " t2_11751 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA\n";
$tmp{"help saf-syn"}.= " name_1 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA\n";
$tmp{"help saf-syn"}.= " name_2 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV.\n";
$tmp{"help saf-syn"}.= " name_22 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV.\n";
$tmp{"help saf-syn"}.= " t2_11751 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV\n";
$tmp{"help saf-syn"}.= " name_1 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV\n";
$tmp{"help saf-syn"}.= "\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= "EXAMPLE 2\n";
$tmp{"help saf-syn"}.= "------------\n";
$tmp{"help saf-syn"}.= " 10 20 30 40 \n";
$tmp{"help saf-syn"}.= " t2_11751 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA\n";
$tmp{"help saf-syn"}.= " name_1 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA\n";
$tmp{"help saf-syn"}.= " name_2 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV.\n";
$tmp{"help saf-syn"}.= " name_22 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV.\n";
$tmp{"help saf-syn"}.= " 50 60 70 80 90\n";
$tmp{"help saf-syn"}.= " t2_11751 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV\n";
$tmp{"help saf-syn"}.= " name_22 .......... .......... .......... ........\n";
$tmp{"help saf-syn"}.= " name_1 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV\n";
$tmp{"help saf-syn"}.= " name_2 .......... NVAGGAPTLP \n";
$tmp{"help saf-syn"}.= " \n";
$tmp{"help saf-syn"}.= " enough?\n";
$tmp{"help saf-syn"}.= " \n";
$tmp{"help fastamul"}= "DES: FASTAmul = Multiple FASTA format (ali, IN | OUT)\n";
$tmp{"help fastamul"}.= "DES: Simply many proteins each in FASTA format.\n";
$tmp{"help fastamul"}.= "DES: \n";
$tmp{"help fastamul"}.= "DES: ***********************************************************\n";
$tmp{"help fastamul"}.= "DES: NOTE: for a correct conversion into alignment formats, all\n";
$tmp{"help fastamul"}.= "DES: sequences have to be aligned already. This implies:\n";
$tmp{"help fastamul"}.= "DES: that ALL sequences have to have IDENTICAL lengths!!\n";
$tmp{"help fastamul"}.= "DES: ***********************************************************\n";
$tmp{"help fastamul"}.= "DES: \n";
$tmp{"help fastamul"}.= "OUT: HSSP|MSF|SAF|FASTA|PIRmul|PIR \n";
$tmp{"help fastamul"}.= "OPT: The following options are available\n";
$tmp{"help fastamul"}.= "OPT: compress -> delete insertions in GUIDE sequence\n";
$tmp{"help fastamul"}.= "OPT: * RESTRICT: for HSSP output, only!!\n";
$tmp{"help fastamul"}.= "OPT: extr=N -> extract sequence of protein N\n";
$tmp{"help fastamul"}.= "OPT: * RESTRICT: for single sequence output, only!\n";
$tmp{"help fastamul"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help fastamul"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help fastamul"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help pirmul"}= "DES: PIRmul = Multiple PIR format (ali, IN | OUT)\n";
$tmp{"help pirmul"}.= "DES: Simply many proteins each in PIR format.\n";
$tmp{"help pirmul"}.= "DES: \n";
$tmp{"help pirmul"}.= "OUT: FASTAmul|FASTA \n";
$tmp{"help pirmul"}.= "OPT: The following options are available\n";
$tmp{"help pirmul"}.= "OPT: extr=N -> extract sequence of protein N\n";
$tmp{"help pirmul"}.= "OPT: * RESTRICT: for single sequence output (FASTA), only!\n";
$tmp{"help pirmul"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help pirmul"}.= "OPT: type 'help frag' for more information on this one\n";
# ------------------------------
# alignment IN
$tmp{"help fssp"}= "DES: FSSP = Definition of Secondary Structure for Proteins format (ali, IN)\n";
$tmp{"help fssp"}.= "OUT: DAF\n";
$tmp{"help fssp"}.= "OPT: The following options are available\n";
$tmp{"help fssp"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help fssp"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help fssp"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
# ------------------------------
# alignment OUT
$tmp{"help daf"}= "DES: DAF = Dirty Alignment Format (ali, OUT)\n";
$tmp{"help daf"}.= "OPT: No options are available (output only HSSP|FSSP -> DAF)\n";
# ------------------------------
# sequence IN / OUT
$tmp{"help dssp"}= "DES: DSSP = Definition of Secondary Structure for Proteins format (seq, IN | OUT)\n";
$tmp{"help dssp"}.= "OUT: FASTA|PIR|MSF|SAF\n";
$tmp{"help dssp"}.= "OPT: The following options are available\n";
$tmp{"help dssp"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help dssp"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help dssp"}.= "OPT: NOTE: if you extract chains, these numbers refer\n";
$tmp{"help dssp"}.= "OPT: to the position in the extracted chain!!\n";
$tmp{"help dssp"}.= "OPT: chain=A,B -> selects only the chains A and B\n";
$tmp{"help dssp"}.= "OPT: NOTE: pass the identifier for chain C as \n";
$tmp{"help dssp"}.= "OPT: file.dssp_C\n";
$tmp{"help dssp"}.= "OPT: providing a chain disables the option 'frag=N-M'\n";
$tmp{"help dssp"}.= "OPT: split -> split HSSP|DSSP|PDB files -> FASTA into chains\n";
$tmp{"help fasta"}= "DES: FASTA format (seq, IN | OUT)\n";
$tmp{"help fasta"}.= "OUT: PIR|GCG\n";
$tmp{"help fasta"}.= "OPT: The following options are available\n";
$tmp{"help fasta"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help fasta"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help fasta"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help pir"}= "DES: PIR = Protein Identification Resource format (seq, IN | OUT)\n";
$tmp{"help pir"}.= "OUT: FASTA|GCG \n";
$tmp{"help pir"}.= "OPT: The following options are available\n";
$tmp{"help pir"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help pir"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help pir"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help gcg"}= "DES: GCG format (seq, IN | OUT)\n";
$tmp{"help gcg"}.= "OUT: PIR|FASTA|FASTAmul|PIRmul \n";
$tmp{"help gcg"}.= "OPT: The following options are available\n";
$tmp{"help gcg"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help gcg"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help gcg"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
# ------------------------------
# sequence IN
$tmp{"help swiss"}= "DES: SWISS = Homology derived Secondary Structure of Proteins format (alignment)\n";
$tmp{"help swiss"}.= "OUT: MSF|DAF|SAF|FASTAmul|PIRmul|PIR|FASTA|GCG \n";
$tmp{"help swiss"}.= "OPT: The following options are available\n";
$tmp{"help swiss"}.= "OPT: expand -> expand the deletion list when writing\n";
$tmp{"help swiss"}.= "OPT: * RESTRICT: for MSF output, only!!\n";
$tmp{"help swiss"}.= "OPT: extr=N -> extract sequence of protein N\n";
$tmp{"help swiss"}.= "OPT: * RESTRICT: for single sequence output, only!\n";
$tmp{"help swiss"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help swiss"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help swiss"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help phdrdb"}= "DES: PHDrdb = PHD.rdb format (seq, IN)\n";
$tmp{"help phdrdb"}.= "OUT: DSSP\n";
$tmp{"help phdrdb"}.= "OUT: Converts PHD rdb file into DSSP formatted file.\n";
$tmp{"help phdrdb"}.= "OUT: NOTE: you have to run PHD with the default or the\n";
$tmp{"help phdrdb"}.= "OUT: option 'both' on the command line\n";
$tmp{"help phdrdb"}.= "OPT: \n";
$tmp{"help phdrdb"}.= "OUT: MSF|PIR|FASTA|GCG|FASTAmul|PIRmul \n";
$tmp{"help phdrdb"}.= "OPT: NOT IMPLEMENTED, yet!\n";
$tmp{"help phdrdb"}.= "OPT: \n";
$tmp{"help phdrdb"}.= "OUT: MSF|PIR|FASTA|GCG|FASTAmul|PIRmul \n";
$tmp{"help phdrdb"}.= "OPT: The following options are available\n";
$tmp{"help phdrdb"}.= "OPT: frag=n-m -> selects fragment from residues N-M\n";
$tmp{"help phdrdb"}.= "OPT: type 'help frag' for more information on this one\n";
$tmp{"help phdrdb"}.= "OPT: * RESTRICT: NOT for DAF formatted output\n";
$tmp{"help phdrdb"}.= "OPT: mergeAli -> provide a valid HSSP file to merge the PHD output\n";
$tmp{"help phdrdb"}.= "OPT: into that one.\n";
$tmp{"help phdrdb"}.= "OPT: \n";
# "------------------------------------------------------------\n";
$tmp{"scrHelpProblems"}= "Maximal protein length:\n";
$tmp{"scrHelpProblems"}.=" $scrName bases upon a FORTRAN program by Reinhard Schneider\n";
$tmp{"scrHelpProblems"}.=" LION Heidelberg), and Ulrike Goebel (now Jena). That pro-\n";
$tmp{"scrHelpProblems"}.=" gram restricts memory space by crashing with proteins of\n";
$tmp{"scrHelpProblems"}.=" more than 6,000 residues. Recompile the FORTRAN program\n";
$tmp{"scrHelpProblems"}.=" to change this feature.\n";
$tmp{"scrHelpProblems"}.=" \n";
$tmp{"scrHelpProblems"}.=" \n";
$tmp{"scrHelpProblems"}.=" \n";
$tmp{"scrHelpProblems"}.=" \n";
} # end of iniHelpLoc
#==============================================================================
# library collected (begin) lll
#==============================================================================
#===============================================================================
sub amino_acid_convert_3_to_1 {
local($three_letter_acid) = @_ ;
local($sbrName3);
$[ =1 ;
#-------------------------------------------------------------------------------
# amino_acid_convert_3_to_1 converts 3 letter alphabet to single letter alphabet
# in: $three_letter_acid
# out: 1|0,msg,$one_letter_acid
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName3="amino_acid_convert_3_to_1";
return(0,"no input to $sbrName3") if (! defined $three_letter_acid);
# initialise translation table
&amino_acid_convert_3_to_1_ini()
if (! %amino_acid_convert_3_to_1);
# not found
return(0,"no conversion for acid=$three_letter_acid!","unk")
if (! defined $amino_acid_convert_3_to_1{$three_letter_acid});
# ok
return(1,"ok",$amino_acid_convert_3_to_1{$three_letter_acid});
} # end of amino_acid_convert_3_to_1
#===============================================================================
sub amino_acid_convert_3_to_1_ini {
#-------------------------------------------------------------------------------
# amino_acid_convert_3_to_1_ini returns GLOBAL array with 3 letter acid -> 1 letter
# out GLOBAL: %amino_acid_convert_3_to_1
#-------------------------------------------------------------------------------
%amino_acid_convert_3_to_1=
(
# amino
'ALA',"A",
'ARG',"R",
'ASN',"N",
'ASP',"D",
'CYS',"C",
'GLN',"Q",
'GLU',"E",
'GLY',"G",
'HIS',"H",
'ILE',"I",
'LEU',"L",
'LYS',"K",
'MET',"M",
'PHE',"F",
'PRO',"P",
'SER',"S",
'THR',"T",
'TRP',"W",
'TYR',"Y",
'VAL',"V",
# nucleic
'A', "A",
'C', "C",
'G', "G",
'T', "T",
);
} # end of amino_acid_convert3_to_1
#==============================================================================
sub brIniErr {
local($local)=@_;
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniErr error check for initial parameters
# in GLOBAL: $par{},@PARAMS
# in: $exceptions = 'kwd1,kwd2'
# key words not to check for file existence
# out: ($Lok,$msg)
#-------------------------------------------------------------------------------
#if( $par{"debug"} ) { cluck( "$scrName:brIniErr" ); }
$sbrName="$scrName:".__FILE__.":".__LINE__.":brIniErr";
@kwd= keys (%par) if (%par);
# ------------------------------
undef %tmp; $#excl=0; # exclude some keyword from check?
@excl=split(/,/,$local) if (defined $local);
if ($#excl>0){
foreach $kwd(@excl){
$tmp{$kwd}=1;}}
$msgHere="";
# ------------------------------
foreach $kwd (@kwd){ # file existence
next if ($kwd =~ /^file(Out|Help|Def)/i);
next if (defined $tmp{$kwd});
if ($kwd=~/^exe/) {
# $msgHere.="*** ERROR executable ($kwd) '".$par{$kwd}."' missing!\n"
# if (! -e $par{$kwd} && ! -l $par{$kwd});
# $msgHere.="*** ERROR executable ($kwd) '".$par{$kwd}."' not executable!\n".
# "*** do the following \t 'chmod +x ".$par{$kwd}."'\n"
# if (-e $par{$kwd} && ! -x $par{$kwd});
}
elsif($kwd=~/^file/){
next if ($par{$kwd} eq "unk" || length($par{$kwd})==0 || !$par{$kwd});
$msgHere.="*** ERROR ".__FILE__.":".__LINE__." file ($kwd) '".$par{$kwd}."' missing!\n"
if (! -e $par{$kwd} && ! -l $par{$kwd});} #
}
if ($msgHere=~/ERROR/){ Carp::confess( $msgHere ); return(0,$msgHere); }
return(1,"ok $sbrName");
} # end of brIniErr
#==============================================================================
sub brIniGetArg {
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniGetArg standard reading of command line arguments
# in GLOBAL: @PARAMS,$defaults{},$par{}
# out GLOBAL: $par{},@fileIn
# out: @arg_not_understood (i.e. returns 0 if everything ok!)
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."brIniGetArg";
$#argUnk=0; # ------------------------------
# (1) get input directory
foreach $arg (@PARAMS){ # search in command line
if ($arg=~/^dirIn=(.+)$/){$par{"dirIn"}=$1;
last;}}
# search in defaults
if ((! defined $par{"dirIn"} || ! -d $par{"dirIn"}) &&
%defaults){
if (defined $defaults{"dirIn"}){
$par{"dirIn"}=$defaults{"dirIn"};
$par{"dirIn"}=$PWD
if (defined $PWD &&
($par{"dirIn"}=~/^(local|unk)$/ || length($par{"dirIn"})==0));}}
$par{"dirIn"}.="/" if (defined $par{"dirIn"} && -d $par{"dirIn"} && $par{"dirIn"}!~/\/$/); # slash
$par{"dirIn"}="" if (! defined $par{"dirIn"} || ! -d $par{"dirIn"}); # empty
# ------------------------------
if (%par){ # all keywords used in script
@tmp=sort keys (%par);}
else{
$#tmp=0;}
$Lverb3=0 if (! defined $Lverb3);
$Lverb2=0 if (! defined $Lverb2);
$#fileIn=0; # ------------------------------
foreach $arg (@PARAMS){ # (2) key word driven input
if ($arg=~/^verb\w*3=(\d)/) {$par{"verb3"}=$Lverb3=$1;}
elsif ($arg=~/^verb\w*3/) {$par{"verb3"}=$Lverb3=1;}
elsif ($arg=~/^verb\w*2=(\d)/) {$par{"verb2"}=$Lverb2=$1;}
elsif ($arg=~/^verb\w*2/) {$par{"verb2"}=$Lverb2=1;}
elsif ($arg=~/^verbose=(\d)/) {$par{"verbose"}=$Lverb=$1;}
elsif ($arg=~/^verbose/) {$par{"verbose"}=$Lverb=1;}
elsif ($arg=~/^not_?([vV]er|[sS]creen)/) {$par{"verbose"}=$Lverb=0; }
else {$Lok=0; # general
# is it file?
if ((-e $arg && ! -d $arg) ||
-l $arg){
$Lok=1;
push(@fileIn,$arg);}
if (! $Lok && length($par{"dirIn"})>1 && -e $par{"dirIn"}.$arg){
$Lok=1;push(@fileIn,$par{"dirIn"}.$arg);}
# any of the paras defined ?
if (! $Lok && $arg=~/=/){
foreach $kwd (@tmp){
if ($arg=~/^$kwd=(.+)$/){$Lok=1;$par{$kwd}=$1;
last;}}}
push(@argUnk,$arg) if (! $Lok);}}
return(@argUnk);
} # end of brIniGetArg
#==============================================================================
sub brIniHelp {
local(%tmp)=@_;
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniHelp initialise help text
# out: \d,txt
# err: 0,$msg -> error
# err: 1,'fin' -> wanted help, given help
# err: 1,$msg -> continue, was just trying
# in: $tmp{} with
# $tmp{sourceFile}= name and path of calling script
# $tmp{scrName}= name of calling script (no .pl)
# $tmp{scrIn}= input arguments for script
# $tmp{scrGoal}= what script does
# $tmp{scrNarg}= number of argument needed for script
# $tmp{scrHelpTxt}= long blabla about script
# separate by '\n'
# $tmp{scrAddHelp}= help option other than standard
# e.g.: "help xyz : explain .xyz "
# many: '\n' separated
# NOTE: this will be an entry to $tmp{$special},
# -> $special = 'help xyz' will give explanation
# $tmp{$special}
# $tmp{special}= 'kwd1,kwd2,...' special keywords
# $tmp{$special}= explanation for $special
# syntax: print flat lines (or '--- $line'), separate by '\n'
# $tmp{scrHelpHints}= hints (tab separated)
# $tmp{scrHelpProblems}= known problems (tab separated)
# in GLOBULAR: @PARAMS
# $par{fileHelpOpt}
# $par{fileHelpMan}
# $par{fileHelpHints}
# $par{fileHelpProblems}
# $par{fileDefautlts}
# in unk: leave undefined, or give value = 'unk'
#-------------------------------------------------------------------------------
$sbrName="lib-br:brIniHelp";
# ------------------------------
# check input
if (0){
foreach $kwd ("sourceFile","scrName","scrIn","scrGoal",
"scrNarg","scrAddHelp","special"){
print "--- input to $sbrName kwd=$kwd, val=",$tmp{$kwd},",\n";}
}
@scrTask=
("--- Task: ".$tmp{"scrGoal"},
"--- ",
"--- Input: ".$tmp{"scrIn"},
# "--- i.e. requires at least ".$tmp{"scrNarg"}.
# " command line argument(s)",
"--- ");
$tmp{"scrNameFull"}=$0 if (! defined $tmp{"scrNameFull"});
# ------------------------------
# additional help keywords?
# ------------------------------
$#tmpAdd=0;
if (defined $tmp{"scrAddHelp"} && $tmp{"scrAddHelp"} ne "unk"){
@tmp=split(/\n/,$tmp{"scrAddHelp"});$Lerr=0;
foreach $tmp(@tmp){
push(@tmpAdd,$tmp{"scrNameFull"}." ".$tmp);
$tmp2=$tmp;$tmp2=~s/^(.+)\s+\:.*$/$1/;$tmp2=~s/\s*$//g;
if (!defined $tmp{"$tmp2"}){
$Lerr=1;
print "-*- WARN $sbrName: miss \$tmp{\$special} for '$tmp2'\n";}}
if ($Lerr){
print
"-*- " x 20,"\n","-*- WARN $sbrName: HELP on HELP\n",
"-*- if you provide special help in tmp{scrAddHelp}, then\n",
"-*- provide also the respective explanation in tmp{\$special},\n",
"-*- where \$special is e.g. 'help xyz' in \n",
"-*- scrAddHelp='help xyz : what to do'\n","-*- " x 20,"\n";}}
# ------------------------------
# build up help standard
# ------------------------------
@scrHelp=
("--- Help: For further information on input options type:",
"--- "." " x length($tmp{"scrNameFull"}).
" ........................................");
@scrHelpLoop=
($tmp{"scrNameFull"}." help : lists all options",
$tmp{"scrNameFull"}." def : writes default settings",
$tmp{"scrNameFull"}." def keyword : settings for keyword",
$tmp{"scrNameFull"}." help keyword : explain key, e.g. 'special', or how for 'how' and 'howie'");
push(@scrHelpLoop,
$tmp{"scrNameFull"}." problems : known problems")
if (! defined $tmp{"s_k_i_p"} || $tmp{"s_k_i_p"} !~ /problems/);
push(@scrHelpLoop,
$tmp{"scrNameFull"}." hints : hints for users")
if (! defined $tmp{"s_k_i_p"} || $tmp{"s_k_i_p"} !~ /hints/);
push(@scrHelpLoop,
$tmp{"scrNameFull"}." manual : will cat the entire manual (... MAY be it will)")
if (! defined $tmp{"s_k_i_p"} || $tmp{"s_k_i_p"} !~ /manual/);
push(@scrHelpLoop,@tmpAdd) if ($#tmpAdd>0);
push(@scrHelp,@scrHelpLoop,
"--- "." " x length($tmp{"scrNameFull"}).
" ........................................");
# ------------------------------
# additional general information
# ------------------------------
$#scrHelpTxtLoc=0;
if (defined $tmp{"scrHelpTxt"}){
@tmp=split(/\n/,$tmp{"scrHelpTxt"});
# '--- scrHelptTxt'
# '> program' i.e. use: '>' to ommitt '--- '
foreach $txt (@tmp){
push(@scrHelpTxtLoc,"--- $txt\n") if ($txt !~ /^[>\%]/);
push(@scrHelpTxtLoc,"$txt\n") if ($txt =~ /^[>\%]/); }}
# ------------------------------
# additional special info
# ------------------------------
$#scrSpecialLoc=0;
if (defined $tmp{"special"}) {
@kwdLoc=split(/,/,$tmp{"special"});
if ($#kwdLoc>1){
foreach $kwd (@kwdLoc){
$tmp=" "; $tmp=$tmp{$kwd} if (defined $tmp{$kwd});
$tmp=~s/\n$//o;
$tmpWrt=sprintf ("--- %-15s %s\n",$kwd,$tmp);
push(@scrSpecialLoc,$tmpWrt); } }}
# ------------------------------
# general:
# ------------------------------
$fstLineLoc= "-" x 80 . "\n";
$fstLineLoc.="--- Perl script $scrName.pl (" . $tmp{"sourceFile"} . ")\n";
$syntaxLoc= "-" x 80 . "\n";
$syntaxLoc.= "--- Syntax used to set parameters by command line:\n";
$syntaxLoc.= "--- 'keyword=value'\n";
$syntaxLoc.= "--- where 'keyword' is one of the following keywords:\n";
# ------------------------------
# no input
if ($#PARAMS < 1) { # ------------------------------
print $fstLineLoc;
print join("\n",@scrTask,"\n");
print @scrHelpTxtLoc;
print join("\n",@scrHelp); print "\n";
return(1,"fin");}
# ------------------------------
# help request
# ------------------------------
elsif ($#PARAMS < 2 && $PARAMS[1] =~ /^(help|man|-m|-h)$/){
print $fstLineLoc;
print join("\n",@scrTask,"\n");
print @scrHelpTxtLoc;
if ($#scrSpecialLoc > 0) {
print "-" x 80,"\n";
print "--- 'special' keywords:\n";
print @scrSpecialLoc,"\n"; }
if (%par) {
@kwdLoc=sort keys (%par);
if ($#kwdLoc>1){
print $syntaxLoc;
$ct=0;print "OPT \t ";
foreach $kwd(@kwdLoc){
++$ct;
printf "%-20s ",$kwd;
if ($ct==4){
$ct=0;print "\nOPT \t ";}}
print "\n";}
print
"--- \n",
"--- you may get further explanations on a particular keyword\n",
"--- by typing:\n",
$tmp{"scrNameFull"}." help keyword\n",
"--- this could explain the key. Type 'how' for info on ".
"'how,howie,show'.\n",
"--- \n";}
else {
print "--- no other options enabled by \%par\n";}
return(1,"fin loop?");}
# ------------------------------
# wants manual
# ------------------------------
elsif ($#PARAMS<2 && $PARAMS[1] eq "manual"){
print $fstLineLoc;
if (defined $par{"fileHelpMan"} && -e $par{"fileHelpMan"}){
open("FHIN",$par{"fileHelpOpt"}) ||
cluck "*** $sbrName: could NOT open file".$par{"fileHelpOpt"};
while(<FHIN>){
print $_;}close(FHIN);}
else {
print "no manual in \%par{'fileHelpMan'}!!\n";}
return(1,"fin");}
# ------------------------------
# wants hints
# ------------------------------
elsif ($#PARAMS==1 && $PARAMS[1] eq "hints"){
print $fstLineLoc;
print "--- Hints for users:\n";$ct=0;
if (defined $par{"fileHelpHints"} && -e $par{"fileHelpHints"}){
open("FHIN",$par{"fileHelpHints"}) ||
cluck "*** $sbrName: could NOT open file".$par{"fileHelpHints"};
while(<FHIN>){
print $_; ++$ct;}close(FHIN);}
if (defined $par{"scrHelpHints"}){
@tmp=split(/\n/,$par{"scrHelpHints"});
foreach $txt(@tmp){print "--- $txt\n";++$ct;}}
if ($ct==0){
print "--- the only hint to give: try another help option!\n";
print "--- sorry ...\n";}
return(1,"fin loop?");}
# ------------------------------
# wants problems
# ------------------------------
elsif ($#PARAMS<2 && $PARAMS[1] eq "problems"){
print $fstLineLoc;
print "--- Known problems with script:\n";$ct=0;
if (defined $par{"fileHelpProblems"} && -e $par{"fileHelpProblems"}){
open("FHIN",$par{"fileHelpProblems"}) ||
cluck "*** $sbrName: could NOT open file".$par{"fileHelpProblems"};
while(<FHIN>){
print $_; ++$ct;}close(FHIN);}
if (defined $par{"scrHelpProblems"}){
@tmp=split(/\n/,$par{"scrHelpProblems"});
foreach $txt(@tmp){print "--- $txt\n";++$ct;}}
if ($ct==0){
print "--- One problem is: there is no problem annotated.\n";
print "--- sorry ...\n";}
return(1,"fin loop?");}
# ------------------------------
# wants default settings
# ------------------------------
elsif ($#PARAMS<2 && $PARAMS[1] eq "def"){
print $fstLineLoc;
if (%par){
@kwdLoc=sort keys (%par);
if ($#kwdLoc>1){
print "--- the default settings are:\n";
printf "--- %-20s %-s\n","." x 20,"." x 20;
printf "--- %-20s = %-s\n","keyword","value";
printf "--- %-20s %-s\n","." x 20,"." x 20;
foreach $kwd(@kwdLoc){
printf "--- %-20s = %-s\n",$kwd,$par{$kwd};}
printf "--- %-20s %-s\n","." x 20,"." x 20;
print
"--- \n",
"--- to get settings for particular keywords use:\n",
$tmp{"scrNameFull"}," def keyword'\n \n";}}
else { print "--- no setting defined in \%par\n";
print "--- sorry...\n";}
return(1,"fin loop?");}
# ------------------------------
# help for particular keyword
# ------------------------------
elsif ($#PARAMS>=2 && $PARAMS[1] eq "help" ||
$#PARAMS==1 && $PARAMS[1] eq "special"){
print $fstLineLoc;
$kwdHelp=$PARAMS[2] if ($#PARAMS > 1);
$kwdHelp=$PARAMS[1] if ($#PARAMS== 1);
$tmp="help $kwdHelp"; # special?
$tmp=~tr/[A-Z]/[a-z]/; # make special keywords case independent
$tmp2=$tmp;$tmp2=~s/help //;
$tmpSpecial=$tmp{"$tmp"} if (defined $tmp{"$tmp"});
$tmpSpecial=$tmp{"$tmp2"} if (! defined $tmp{"$tmp"} && defined $tmp{"$tmp2"});
$#kwdLoc=$#expLoc=0; # (1) get all respective keywords
if (%par && $kwdHelp ne "special"){
@kwdLoc=keys (%par);$#tmp=0;
foreach $kwd (@kwdLoc){
push(@tmp,$kwd) if ($kwd =~/$kwdHelp/i);}
@kwdLoc=sort @tmp;}
# (2) is there a 'help option file' ?
if (defined $par{"fileHelpOpt"} && -e $par{"fileHelpOpt"} &&
$kwdHelp ne "special"){
print $syntaxLoc;
open("FHIN",$par{"fileHelpOpt"}) ||
cluck "*** $sbrName: could NOT open file".$par{"fileHelpOpt"};
while(<FHIN>){
next if ($_=~/^\#/);
$line=$_;
$tmp=$_;$tmp=~s/\s//g;
next if (length($tmp)<2);
next if ($_=~/^\s/ && ! $Lok);
if ($Lok && $_=~/^\s/){
print $_;
next;}
elsif ($Lok && $_!~/^\s/){
$Lok=0;}
if (! $Lok && $_ !~ /^[\s\t]+/){
$line=$_;
($tmp1,$tmp2)=split(/[\s\t]+/,$_);
$Lok=1 if (length($tmp1)>1 && $tmp1 =~ /$kwdHelp/i);
print $line if ($Lok);}}close(FHIN);
print "-" x 80, "\n";}
# (3) is there a default file?
elsif (defined $par{"fileDefaults"} && -e $par{"fileDefaults"} &&
$kwdHelp ne "special"){
($Lok,$msg,%def)=&brIniRdDef($par{"fileDefaults"});
$def{"kwd"}="" if (! $Lok); # hack: short cut error
@kwdLoc=split(/,/,$def{"kwd"});$#tmp=0;
foreach $kwd (@kwdLoc){
if ($kwd =~/$kwdHelp/i){
push(@tmp,$kwd);
if (defined $def{$kwd,"expl"}){
$def{$kwd,"expl"}=~s/\n/\n--- /g;
push(@expLoc,$def{$kwd,"expl"});}
else {
push(@expLoc," ");}}}
@kwdLoc=@tmp;}
# (4) else: read itself
elsif ($kwdHelp ne "special"){
($Lok,$msg,%def)=
&brIniHelpRdItself($tmp{"sourceFile"});
Carp::confess('..... verrry sorry the option blew up ... ') if (! $Lok);
$def{"kwd"}="" if (! $Lok); # hack: short cut error
@kwdLoc=split(/,/,$def{"kwd"});$#tmp=0;
foreach $kwd (@kwdLoc){
next if ($kwd !~/$kwdHelp/i && $kwdHelp !~ /$kwd/ );
push(@tmp,$kwd);
if (defined $def{$kwd}){
$def{$kwd}=~s/\n[\t\s]*/\n--- /g;
push(@expLoc,$def{$kwd});}
else {push(@expLoc," ");}}
@kwdLoc=@tmp;}
$Lerr=1;
if ($#kwdLoc>0){ # (4) write the stuff
printf "--- %-20s %-s\n","." x 20,"." x 53;
printf "--- %-20s %-s\n","keyword","explanation";
printf "--- %-20s %-s\n","." x 20,"." x 53;
foreach $it(1..$#kwdLoc){
$tmp=" "; $tmp=$expLoc[$it] if (defined $expLoc[$it]);
printf "--- %-20s %-s\n",$kwdLoc[$it],$tmp;}
printf "--- %-20s %-s\n","." x 20,"." x 53;
print "--- \n";$Lerr=0;}
# (5) special help?
if (defined $tmpSpecial ||
($kwdHelp eq "special" && defined $tmp{"special"})){
print "--- Special help for '$kwdHelp':\n";
if ($kwdHelp eq "special"){
print @scrSpecialLoc,"\n";}
else {
foreach $scrSpecialLoc (@scrSpecialLoc) {
$scrSpecialLoc=~s/\n$//;
next if ($scrSpecialLoc !~ /$kwdHelp/);
print "$scrSpecialLoc";}
print "\n";}
$Lerr=0;
return(1,"fin") if ($kwdHelp eq "special");}
print "--- sorry, no explanations found for keyword '$kwdHelp'\n" if ($Lerr);
return(1,"fin loop?");}
# ------------------------------
# wants settings for keyword
# ------------------------------
elsif ($#PARAMS>=2 && $PARAMS[1] eq "def"){
$kwdHelp=$PARAMS[2];
print "-" x 80, "\n"; print "--- Perl script $scrName.pl (",$tmp{"sourceFile"},")\n";
if (%par){
@kwdLoc=sort keys (%par);
if ($#kwdLoc>1){
print "--- the default settings are:\n";
printf "--- %-20s %-s\n","." x 20,"." x 53;
printf "--- %-20s = %-s\n","keyword","value";
printf "--- %-20s %-s\n","." x 20,"." x 53;
foreach $kwd(@kwdLoc){
next if ($kwd !~ /$kwdHelp/);
printf "--- %-20s = %-s\n",$kwd,$par{$kwd};}
printf "--- %-20s %-s\n","." x 20,"." x 53;
print " \n";}}
else { print "--- sorry, no setting defined in \%par\n";}
return(1,"fin loop?");}
return(1,"ok $sbrName");
} # end of brIniHelp
#==============================================================================
sub brIniHelpLoop {
local($promptLoc,%tmp)=@_;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniHelpLoop loop over help
# in/out: see brIniHelp
# out: 1|0,msg, implicit:
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."brIniHelpLoop";$fhinLoc="FHIN_"."brIniHelpLoop";
($Lok,$msg)= # want help?
&brIniHelp(%tmp);
return(&errSbrMsg("after brIniHelp",$msg)) if (! $Lok);
# ------------------------------
# loop over help
# ------------------------------
if ($msg =~ /^fin loop/) {
$#tmp=0;
foreach $txt (@scrHelpLoop) { $txt=~s/^.*\.pl\s*//g;
push(@tmp,$txt); }
@scrHelpLoop2=@tmp;
$Lquit=0;
$def="help";
$ct=0;
while (! $Lquit) {
printf "%-s %-s\n", $promptLoc,"-" x (79 - length($promptLoc));
printf "%-s %-15s %-s\n",$promptLoc,"", "Interactive help";
printf "%-s %-15s %-s\n",$promptLoc,"OPTIONS","";
foreach $txt (@scrHelpLoop2) {
printf "%-s %-15s %-s\n",$promptLoc," ",$txt; }
printf "%-s %-15s %-s\n",$promptLoc,"","";
printf "%-s %-15s %-s\n",$promptLoc,"ABBREVIATIONS", "h=help, d=def (e.g. 'h kwd')";
printf "%-s %-15s %-s\n",$promptLoc,"ENOUGH ?", "[quit|q|e|exit] to end";
$def="$PARAMS[1]" if (defined $def); # take previous
$ansr=
&get_in_keyboard("type",$def,$promptLoc);
# <--- QUIT
$tmp=$ansr;$tmp=~s/\s//g;
if ($ansr=~/^[q|quit|e|exit]$/) {
$Lquit=1;
last; }
# redefine @PARAMS
@PARAMS=split(/\s+/,$ansr);
$PARAMS[1]="help" if ($PARAMS[1] eq "h" || $PARAMS[1] eq "H");
$PARAMS[1]="def" if ($PARAMS[1] eq "d" || $PARAMS[1] eq "D");
++$ct;
# add keyword help
if ($ct > 1 && $#PARAMS < 2) {
$PARAMS[2]=$PARAMS[1];
$PARAMS[1]="help";}
$txt1="start again with(";
$txt2=join(' ',@PARAMS);
$lenfin=80 - 6 - (length($txt1) + length($txt2));
print "--- ","-" x length($txt1),"#" x length($txt2),"--", "-" x $lenfin,"\n";
print "--- ",$txt1,$txt2,")\n";
print "--- ","-" x length($txt1),"#" x length($txt2),"--", "-" x $lenfin,"\n";
# call again
($Lok,$msg)=
&brIniHelp(%tmp); return(&errSbrMsg("after brIniHelp",$msg)) if (! $Lok);
# <--- QUIT
$Lquit=1 if ($msg eq "fin");
}
$msg="fin";
}
return(1,$msg);
} # end of brIniHelpLoop
#==============================================================================
sub brIniHelpRdItself {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniHelpRdItself reads the calling perl script (scrName),
# searches for 'sub\siniDef', and gets comment lines
# in: perl-script-source
# out: (Lok,$msg,%tmp), with:
# $tmp{"kwd"} = 'kwd1,kwd2'
# $tmp{"$kwd1"} = explanations for keyword 1
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."brIniHelpRdItself";$fhinLoc="FHIN_"."brIniHelpRdItself";
$Lok= &open_file("$fhinLoc","$fileInLoc");
return(0,"*** ERROR $sbrName: old '$fileInLoc' not opened\n") if (! $Lok);
# read file
while (<$fhinLoc>) { # search for initialising subroutine
last if ($_=/^su[b] iniDef.* \{/);}
$Lis=0;undef %tmp; $#tmp=0;
while (<$fhinLoc>) { # read lines with ' %par{"kwd"}= $val # comment '
$_=~s/\n//g;
last if ($_=~/^su[b] .*\{/ && $_!~/^su[b] iniDef.* \{/);
# new expression
if ($_=~/[\s\t]+\$par\{[\"\']?([^\"\'\}]+)[\"\']?\}[^\#]*\#\s*(.*)$/){
$Lis=1;$kwd=$1; push(@tmp,$kwd);
$tmp{$kwd}=$2 if (defined $2);}
# end if only '------' line
elsif ($Lis && defined $tmp{$kwd} && $_=~/^[\s\t]+\# ?\-+/){
$Lis=0;}
# add to previous (only if it had an explanation)
elsif ($Lis && defined $tmp{$kwd} && $_=~/^[\s\t]*\# (.*)$/){
$tmp{$kwd}.="\n".$1;}
# end if nothing followed
elsif ($Lis){
$Lis=0;}}close($fhinLoc);
$tmp{"kwd"}=join(',',@tmp);
return(1,"ok $sbrName",%tmp);
} # end of brIniHelpRdItself
#==============================================================================
sub brIniRdDef {
local ($fileLoc)=@_;
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniRdDef reads defaults for initialsing parameters
# in GLOBAL: $par{},@PARAMS
# out GLOBAL: $par{} (i.e. changes settings automatically)
# in: file_default
# out: ($Lok,$msg,%defaults) with:
# $defaults{"kwd"}= 'kwd1,kwd2,...,'
# $defaults{"$kwd1"}= val1
# $defaults{"$kwd1","expl"}=explanation for kwd1
# note: long explanations split by '\n'
#-------------------------------------------------------------------------------
$sbrName="lib-br:brIniRdDef"; $fhin="FHIN_brIniRdDef";
&open_file("$fhin","$fileLoc") ||
return(0,"*** ERROR $sbrName: failed to open in '$fileLoc'\n");
undef %defaults; $#kwd=0; $Lis=0;
# ------------------------------
while (<$fhin>){ # read file
next if (length($_)<3 || $_=~/^\#/ || $_!~/\t/); # ignore lines beginning with '#'
$_=~s/\n//g;
$line=$_;
$tmp=$line; $tmp=~s/[\s\#\-\*\.\=\t]//g;
# ignore lines with only spaces or '-|#|*|='
next if (length($tmp)<1);
# purge leading blanks and tabs
$line=~s/^[\s\t]*|[\s\t]*$//g;
# ------------------------------
# (1) case 'kwd val # comment'
if ($line=~/^([^\s\t]+)[\s\t]+([^\s\t]+)[\s\t]+\# ?(.*)$/){
$kwd=$1; push(@kwd,$kwd); $defaults{$kwd}=$2;
$defaults{$kwd,"expl"}=$3 if (defined $3 && length($3)>1); $Lis=1;}
# (2) case 'kwd val'
elsif ($line=~/^([^\s\t]+)[\s\t]+([^\s\t]+)[\s\t]*$/){
$kwd=$1; $defaults{$kwd}=$2; $Lis=1; $defaults{$kwd,"expl"}=""; }
# (3) case ' # ----'
elsif ($Lis && $line =~ /^\#\s*[\-\=\_\.\*]+/){
$Lis=0;}
elsif ($Lis && defined $defaults{$kwd,"expl"} && $line =~ /^\#\s*(.*)$/){
$defaults{$kwd,"expl"}.="\n".$1;}}
close($fhin);
# ------------------------------
foreach $kwd (@kwd){ # fill in wild cards
$defaults{$kwd}=$ARCH if ($defaults{$kwd}=~/ARCH/);}
# ------------------------------
foreach $kwd (@kwd){ # complete it
$defaults{$kwd,"expl"}=" " if (! defined $defaults{$kwd,"expl"});}
$defaults{"kwd"}=join(',',@kwd);
# ------------------------------
# check the defaults read
# AND OVERWRITE $par{} !!
@kwdDef=keys %par; foreach $kwd (@kwdDef){ $tmp{$kwd}=1;}
$Lok=1;
foreach $kwd (@kwd){
if (! defined $tmp{$kwd}){
$Lok=0;
print
"*** ERROR $sbrName: wrong keyword ($kwd) in defaults file ",
$par{"fileDefaults"},"\n";}
# ******************************
else { # overwrite
# ******************************
$par{$kwd}=$defaults{$kwd};}}
return(0,"*** ERROR $sbrName failed finishing to read defaults file\n") if (! $Lok);
return(1,"ok $sbrName",%defaults);
} # end of brIniRdDef
#==============================================================================
sub brIniSet {
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniSet changing parameters according to input arguments
# e.g. adding directories to file names asf
#-------------------------------------------------------------------------------
$sbrName="lib-br:brIniSet";
@kwd=sort keys(%par) if (%par);
# ------------------------------
$#tmp=0; # purge empty keywords
foreach $kwd (@kwd){
if (defined $kwd && length($kwd)>=1 && defined $par{$kwd}){
push(@tmp,$kwd);}
else {
print "-*- WARN $sbrName: for kwd '$kwd', par{kwd} not defined!\n";}}
@kwd=@tmp;
# jobId
$par{"jobid"}=$$
if (! defined $par{"jobid"} || $par{"jobid"} eq 'jobid' || length($par{"jobid"})<1);
# ------------------------------
# add jobid
foreach $kwd (@kwd){
$par{$kwd}=~s/jobid/$par{"jobid"}/;}
# ------------------------------
# WATCH it for file lists: add dirIn
if (defined $par{"dirIn"} && $par{"dirIn"} ne "unk" && $par{"dirIn"} ne "local"
&& length($par{"dirIn"})>1){
foreach $fileIn(@fileIn){
$fileIn=$par{"dirIn"}.$fileIn if (! -e $fileIn);
if (! -e $fileIn){ print
"*** $sbrName: no fileIn=$fileIn, dir=",$par{"dirIn"},",\n";
return(0);}}}
$#kwdFileOut=0; # ------------------------------
foreach $kwd (@kwd){ # add 'pre' 'title' 'ext' to output files not specified
next if ($kwd !~ /^fileOut/);
push(@kwdFileOut,$kwd);
next if (defined $par{$kwd} && $par{$kwd} ne "unk" && length($par{$kwd})>0);
$kwdPre=$kwd; $kwdPre=~s/file/pre/; $kwdExt=$kwd; $kwdExt=~s/file/ext/;
$pre="";$pre=$par{"$kwdPre"} if (defined $par{"$kwdPre"});
$ext="";$ext=$par{"$kwdExt"} if (defined $par{"$kwdExt"});
if (! defined $par{"title"} || $par{"title"} eq "unk"){
$par{"title"}=$scrName;$par{"title"}=~tr/[a-z]/[A-Z]/;} # capitalize title
$par{$kwd}=$pre.$par{"title"}.$ext;}
# ------------------------------
# add output directory
if (defined $par{"dirOut"} && $par{"dirOut"} ne "unk" && $par{"dirOut"} ne "local"
&& length($par{"dirOut"})>1){
if (! -d $par{"dirOut"}){ # make directory
print "--- $sbrName mkdir ",$par{"dirOut"},"\n" if ($par{"verb2"});
$tmp=$par{"dirOut"};$tmp=~s/\/$// if ($tmp=~/\/$/);
$Lok= mkdir ($tmp,umask);
print
"*** $sbrName failed making directory '",
$par{"dirOut"},"'\n" if (! $Lok);}
# add slash
$par{"dirOut"}.="/" if (-d $par{"dirOut"} && $par{"dirOut"} !~/\/$/);
foreach $kwd (@kwdFileOut){
next if ($par{$kwd} =~ /^$par{"dirOut"}/);
next if ($par{$kwd} eq "unk" || ! $par{$kwd});
$par{$kwd}=$par{"dirOut"}.$par{$kwd} if (-d $par{"dirOut"});}}
# ------------------------------
# push array of output files
$#fileOut=0 if (! defined @fileOut);
foreach $kwd (@kwdFileOut){
push(@fileOut,$par{$kwd});}
# ------------------------------
# temporary files: add work dir
if( !$par{dirWork} ){ $par{dirWork} = File::Temp::tempdir( CLEANUP => !$par{debug} ); }
if (defined $par{"dirWork"} && $par{"dirWork"} ne "unk" && $par{"dirWork"} ne "local"
&& length($par{"dirWork"})>1) {
if (! -d $par{"dirWork"}){ # make directory
print "--- $sbrName mkdir ",$par{"dirWork"},"\n" if ($par{"verb2"});
$tmp=$par{"dirWork"};$tmp=~s/\/$// if ($tmp=~/\/$/);
$Lok= mkdir ($tmp,umask);
print
"*** $sbrName failed making directory '",$par{"dirWork"},"'\n" if (! $Lok);}
$par{"dirWork"}.="/" if (-d $par{"dirWork"} && $par{"dirWork"} !~/\/$/); # add slash
foreach $kwd (@kwd){
next if ($kwd !~ /^file/);
next if ($kwd =~ /^file(In|Out|Help|Def|Mat)/i); # lkajan: infernal. This should be a next UNLESS /something/ condition.
$par{$kwd}=~s/jobid/$par{"jobid"}/ ;
next if ($par{$kwd} =~ /^$par{"dirWork"}/);
$par{$kwd}=$par{"dirWork"}.$par{$kwd};}}
# ------------------------------
# blabla
$Lverb=1 if (defined $par{"verbose"} && $par{"verbose"});
$Lverb2=1 if (defined $par{"verb2"} && $par{"verb2"});
$Lverb3=1 if (defined $par{"verb3"} && $par{"verb3"});
# ------------------------------
# add ARCH
if (defined $ARCH || defined $par{"ARCH"}){
$ARCH=$par{"ARCH"} if (! defined $ARCH && defined $par{"ARCH"});
$par{"ARCH"}=$ARCH if ( defined $ARCH && ! defined $par{"ARCH"});
foreach $kwd (@kwd){ # add directory to executables
next if ($kwd !~ /^exe/);
next if ($par{$kwd} !~ /ARCH/);
$par{$kwd}=~s/ARCH/$ARCH/;}}
# ------------------------------
foreach $kwd (@kwd){ # add directory to executables
next if ($kwd !~/^exe/);
next if (-e $par{$kwd} || -l $par{$kwd});
# try to add perl script directory
next if (! defined $par{"dirPerl"} || ! -d $par{"dirPerl"});
next if ($par{$kwd}=~/$par{"dirPerl"}/); # did already, no result
$tmp=$par{"dirPerl"}; $tmp.="/" if ($tmp !~ /\/$/);
$tmp=$tmp.$par{$kwd};
next if (! -e $tmp && ! -l $tmp);
$par{$kwd}=$tmp; }
# ------------------------------
# priority
if (defined $par{"optNice"} && $par{"optNice"} ne " " && length($par{"optNice"})>0){
$niceNum="";
if ($par{"optNice"}=~/nice\s*-/){
$par{"optNice"}=~s/nice-/nice -/;
$niceNum=$par{"optNice"};$niceNum=~s/\s|nice|\-|\+//g; }
elsif ($par{"optNice"}=~/^\d+$/){
$niceNum=$par{"optNice"};}
$niceNum=~s/\D//g;
setpriority(0,0,$niceNum) if (length($niceNum)>0); }
return(1);
} # end of brIniSet
#==============================================================================
sub brIniWrt {
local($exclLoc,$fhTraceLocSbr)=@_;
$[ =1 ;
#-------------------------------------------------------------------------------
# brIniWrt write initial settings on screen
# in: $excl : 'kwd1,kwd2,kw*' exclude from writing
# '*' for wild card
# in: $fhTrace : file handle to write
# = 0, or undefined -> STDOUT
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."brIniWrt";
return(0,"*** $sbrName: no settings defined in %par\n") if (! %par);
$fhTraceLocSbr="STDOUT" if (! defined $fhTraceLocSbr || ! $fhTraceLocSbr);
if (defined $Date) {
$dateTmp=$Date; }
else {
$tmp=`date`; $tmp=~s/\n//g if (defined $tmp);
$dateTmp=$tmp || "before year 2000"; }
print $fhTraceLocSbr "--- ","-" x 80, "\n";
print $fhTraceLocSbr "--- Initial settings for $scrName ($0) on $dateTmp:\n";
@kwd= sort keys (%par);
# ------------------------------
# to exclude
@tmp= split(/,/,$exclLoc) if (defined $exclLoc);
$#exclLoc=0; undef %exclLoc;
foreach $tmp (@tmp) {
if ($tmp !~ /\*/) { # exact match
$exclLoc{"$tmp"}=1; }
else { # wild card
$tmp=~s/\*//g;
push(@exclLoc,$tmp); } }
if ($#exclLoc > 0) {
$exclLoc2=join('|',@exclLoc); }
else {
$exclLoc2=0; }
$#kwd2=0; # ------------------------------
foreach $kwd (@kwd) { # parameters
next if (! defined $par{$kwd});
next if ($kwd=~/expl$/);
next if (length($par{$kwd})<1);
if ($kwd =~/^fileOut/) {
push(@kwd2,$kwd);
next;}
next if ($par{$kwd} eq "unk");
next if (defined $exclLoc{$kwd}); # exclusion required
next if ($exclLoc2 && $kwd =~ /$exclLoc2/);
printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}
# ------------------------------
if ($#kwd2>0){ # output files
print $fhTraceLocSbr "--- \n","--- Output files:\n";
foreach $kwd (@kwd2) {
next if ($par{$kwd} eq "unk"|| ! $par{$kwd});
next if (defined $exclLoc{$kwd}); # exclusion required
next if ($exclLoc2 && $kwd =~ /$exclLoc2/);
printf $fhTraceLocSbr "--- %-20s '%-s'\n",$kwd,$par{$kwd};}}
# ------------------------------
# input files
if (defined @fileIn && $#fileIn>1){
# get dirs
$#tmpdir=0; undef %tmpdir;
foreach $file (@fileIn){
if ($file =~ /^(.*\/)[^\/]/){
$tmp=$1;$tmp=~s/\/$//g;
if (! defined $tmpdir{$tmp}){push(@tmpdir,$tmp);
$tmpdir{$tmp}=1;}}}
# write
print $fhTraceLocSbr "--- \n";
printf $fhTraceLocSbr "--- %-20s number =%6d\n","Input files:",$#fileIn;
printf $fhTraceLocSbr "--- %-20s dirs =%-s\n","Input dir:", join(',',@tmpdir)
if ($#tmpdir == 1);
printf $fhTraceLocSbr "--- %-20s dirs =%-s\n","Input dirs:",join(',',@tmpdir)
if ($#tmpdir > 1);
for ($it=1;$it<=$#fileIn;$it+=5){
print $fhTraceLocSbr "--- IN: ";
$it2=$it;
while ( $it2 <= $#fileIn && $it2 < ($it+5) ){
$tmp=$fileIn[$it2]; $tmp=~s/^.*\///g;
printf $fhTraceLocSbr "%-18s ",$tmp;++$it2;}
print $fhTraceLocSbr "\n";}}
elsif ((defined @fileIn && $#fileIn==1) || (defined $fileIn && -e $fileIn)){
$tmp=0;
$tmp=$fileIn if (defined $fileIn && $fileIn);
$tmp=$fileIn[1] if (! $tmp && defined @fileIn && $#fileIn==1);
print $fhTraceLocSbr "--- \n";
printf $fhTraceLocSbr "--- %-20s '%-s'\n","Input file:",$tmp;}
print $fhTraceLocSbr "--- \n";
printf $fhTraceLocSbr "--- %-20s %-s\n","excluded from write:",$exclLoc
if (defined $exclLoc);
print $fhTraceLocSbr "--- \n","--- ","-" x 80, "\n","--- \n";
return(1,"ok $sbrName");
} # end of brIniWrt
#===============================================================================
sub bynumber {
#-------------------------------------------------------------------------------
# bynumber function sorting list by number
#-------------------------------------------------------------------------------
$a<=>$b;
} # end of bynumber
#===============================================================================
sub bynumber_high2low {
#-------------------------------------------------------------------------------
# bynumber_high2low function sorting list by number (start with high)
#-------------------------------------------------------------------------------
$b<=>$a;
} # end of bynumber_high2low
#==============================================================================
sub complete_dir { return(&completeDir(@_)); } # alias
#===============================================================================
sub completeDir {local($DIR)=@_; $[=1 ;
return(0) if (! defined $DIR);
return($DIR) if ($DIR =~/\/$/);
return($DIR."/");} # end of completeDir
#==============================================================================
sub convFastamul2many {
local($fileInLoc,$fileOutLoc,$formOutLoc,$fragLoc,$extrLoc,$fhErrSbr,
$LdoCompressLoc,$LshortNamesLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convFastamul2msf converts FASTAmul into many formats: FASTA,MSF,PIR,SAF,PIRmul
# in: $fileInLoc,$fileOutLoc,$formOutLoc,$fragLoc,$extrLoc,$fhErrSbr
# in: $formOutLoc format MSF|FASTA|PIR
# in: $fragLoc=n-m fragment to extract (optional)
# in: $extrLoc=i,j,k take only sequences i,j,k from PIRmul
# in: NOTE: to leave blank =0, e.g.
# in: 'file.fastamul,file.f,0,5' would get fifth sequence
# in: $LdoCompressLoc delete insertions in master
# in: $LshortNamesLoc: if 1 names <=15 characters
# out: implicit: file written
# err: (1,'ok'), (0,'message')
# err: e: (1,msg) -> ok
# err: a: (0,msg) -> some arguments missing/files not opened
# err: b: (2,msg) -> no output file written
# err: b: (3,msg) -> ERROR from msfCheckFormat
# specification of format see interpretSeqFastamul
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."convFastamul2msf";$fhinLoc="FHIN_"."convFastamul2msf";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOutLoc!") if (! defined $formOutLoc);
$fragLoc=0 if (! defined $fragLoc);
$extrLoc=0 if (! defined $extrLoc);
$LdoCompressLoc=0 if (! defined $LdoCompressLoc);
$LshortNamesLoc=0 if (! defined $LshortNamesLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# interpret input
$formOutLoc=~tr/[A-Z]/[a-z]/;
if ($fragLoc){
$fragLoc=~s/\s//g;
return(0,"*** $sbrName: syntax of fragLoc ($fragLoc) must be :\n".
" 'ifir-ilas', where ifir,ilas are integers (or 1-*)\n")
if ($fragLoc && $fragLoc !~/[\d\*]\-[\d\*]/);}
if ($extrLoc){
$extrLoc=~s/\s//g;
return(0,"*** $sbrName: syntax of extrLoc ($extrLoc) must be :\n".
" 'n1,n2,n3-n4', where n* are integers\n")
if ($extrLoc && $extrLoc =~/[^0-9\-,]/);
@extr=&get_range($extrLoc);
undef %take;
foreach $it(@extr){
$take{$it}=1;}}
# open file
open($fhinLoc,$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) ||
return(0,"*** ERROR $sbrName: fileIn=$fileInLoc, not opened\n");
# ------------------------------
undef %fasta; $ct=$#id=0; # read file
while (<$fhinLoc>) {
$_=~s/\n//g;
if ($_=~/^\s*\>\s*(.*)$/){ # is id
$name=$1;$name=~s/[\s\t]+/ /g; # purge too many blanks
$name=~s/^\s*|\s*$//g; # purge leading blanks
$id=$name;$id=~s/^(\S+).*$/$1/; # shorter identifier
++$ct;
$id="$ct" if (length($id)<1);
push(@id,$id);
$fasta{"id",$ct}= $name;
$fasta{"seq",$ct}="";}
else { # is sequence
$_=~s/\s|\t//g;
$fasta{"seq",$ct}.=$_;}}
# ------------------------------
undef %tmp; $ctTake=0; # store names for passing variables
foreach $it (1..$#id){
next if ($extrLoc && (! defined $take{$it} || ! $take{$it}));
++$ctTake;
$tmp{"id",$ctTake}= $fasta{"id",$it};
$tmp{"seq",$ctTake}=$fasta{"seq",$it};}
$tmp{"NROWS"}=$ctTake;
%fasta=%tmp;
undef %tmp;
# ------------------------------
# compress
# ------------------------------
if ($LdoCompressLoc){
$ctcleave=$ctres=0;
$lenloc=length($fasta{"seq",1});
# all 0
foreach $itprot (1..$fasta{"NROWS"}){
$fasta{"new",$itprot}="";
}
# loop over all residues
foreach $itres (1..$lenloc){
# is residue
if (substr($fasta{"seq",1},$itres,1)=~/^[A-Za-z]/){
foreach $itprot (1..$fasta{"NROWS"}){
$fasta{"new",$itprot}.=substr($fasta{"seq",$itprot},$itres,1);
}
++$ctres;
next;}
# seems insertion
++$ctcleave;
}
# check: sum ok?
return(0,"*** $sbrName: failed at compressing ncleave=$ctcleave, nresnew=$ctres,".
" before=".$lenloc." file=$fileInLoc!")
if ($lenloc != ($ctcleave + $ctres));
# replace by cleaved version
foreach $itprot (1..$fasta{"NROWS"}){
$fasta{"seq",$itprot}=$fasta{"new",$itprot};
}}
$ctres=length($fasta{"seq",1});
# ------------------------------
# shorten names?
# ------------------------------
if ($LshortNamesLoc){
undef %fasta2;
foreach $it (1..$fasta{"NROWS"}){
if (length($fasta{"id",$it})<=15) {
$fasta2{$fasta{"id",$it}}=1;
next;}
# too long
$id=$fasta{"id",$it};
$id=~s/^.*\|//g; # purge paths
# purge blanks
$id=~s/\s//g if (length($id)>15);
# purge extensions
$id=~s/\.[a-z]//g if (length($id)>15);
# cleave
if (length($id)>15){
$id=substr($id,1,15);}
# not unique
if (defined $fasta2{$id}){
$id=substr($id,1,12);
$ct=1;$idfasta=$id.$ct;
while(defined $fasta2{$idfasta}){
++$ct;
last if ($ct>999);}
$id=$idfasta;}
return(0,"*** $sbrName: shoot id=$id, orig=",,", failed shortening\n")
if (defined $fasta2{$id} || length($id)>15);
$fasta2{$id}=1;
$fasta{"id",$it}=$id;
}
undef %fasta2; }
# ------------------------------
# select subsets
# ------------------------------
if ($fragLoc){
($beg,$end)=split('-',$fragLoc);$len=length($fasta{"seq","1"});
$beg=1 if ($beg eq "*"); $end=$len if ($end eq "*");
if ($len< ($end-$beg+1)){
print
"-*- WARN $sbrName: $beg-$end not possible, as length of protein=$len\n";}
else {
foreach $it (1..$fasta{"NROWS"}){
$fasta{"seq",$it}=substr($fasta{"seq",$it},$beg,($end-$beg+1));}}}
# --------------------------------------------------
# write output
# --------------------------------------------------
# ------------------------------
# write an MSF formatted file
if ($formOutLoc eq "msf"){
undef %tmp; undef %tmp2;
foreach $it (1..$fasta{"NROWS"}){
$name= $fasta{"id",$it};
$name=~s/^\s*|\s*$//g;$name=~s/^(\S+).*$/$1/g;
$name=substr($name,1,14) if (length($name)>14); # yy hack for convert_seq
if (defined $tmp2{$name}){ # avoid duplication
$ct=0;while (defined $tmp2{$name}){
++$ct;$name=substr($name,1,12).$ct;}}$tmp2{$name}=1;
$tmp{$it}= $name;
$tmp{SEQS}->{$name}= $fasta{"seq",$it}; }
$tmp{"NROWS"}=$fasta{"NROWS"};
$tmp{"FROM"}=$fileInLoc;
$tmp{"TO"}= $fileOutLoc;
$fhout="FHOUT_MSF_FROM_SAF";
open("$fhout",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) || # open file
return(0,"*** $sbrName cannot open fileOutLoc=$fileOutLoc\n");
$Lok=
&msfWrt($fhout,%tmp); # write the file
close("$fhout");
return(0,"*** ERROR $sbrName: failed in MSF format ($fileOutLoc)\n") if (! $Lok);}
# ------------------------------
# write a SAF,PIR,FASTA, formatted file
elsif ($formOutLoc eq "saf" || $formOutLoc eq "fastamul" || $formOutLoc eq "pirmul" ||
$formOutLoc eq "fasta" || $formOutLoc eq "pir" || $formOutLoc eq "gcg"){
if ($formOutLoc =~ /^fasta/){
($Lok,$msg)=&fastaWrtMul($fileOutLoc,%fasta);}
elsif ($formOutLoc =~ /^pir/){
($Lok,$msg)=&pirWrtMul($fileOutLoc,%fasta);}
elsif ($formOutLoc eq "saf"){
($Lok,$msg)=&safWrt($fileOutLoc,%fasta);}
elsif ($formOutLoc eq "gcg"){
($Lok,$msg)=&gcgWrt($fileOutLoc,$fasta{"id","1"},$fasta{"seq","1"});}
return(0,"*** ERROR $sbrName: failed in FASTA format ($fileOutLoc)\n".$msg."\n")
if (! $Lok);}
# ------------------------------
# file existing??
return(2,"*** $sbrName ERROR after write, missing fileOutLoc=$fileOutLoc\n")
if (! -e $fileOutLoc);
# ------------------------------
# make a basic test of msf format
if ($formOutLoc eq "msf"){
($Lok,$msg)=
&msfCheckFormat($fileOutLoc);
return(3,"$msg"."*** $sbrName ERROR from msfCheckFormat fileOutLoc=$fileOutLoc\n") if (! $Lok);}
# ------------------------------
$#fasta=$#nameLoc=0; # save space
undef %fasta; undef %nameInBlock; undef %tmp;
return(1,"$sbrName ok");
} # end of convFastamul2many
#==============================================================================
sub convFssp2Daf {
local ($fileFssp,$fileDaf,$fileDafTmp,$exeConv,$dirDsspLoc) = @_ ;
local ($fhinLoc,$fhoutLoc,$tmp,@tmp);
$[ =1 ;
#--------------------------------------------------------------------------------
# convFssp2Daf converts an HSSP file into the DAF format
# in: fileHssp, fileDaf, execonvFssp2Daf
# out: 1 if converted file in DAF and existing, 0 else
#--------------------------------------------------------------------------------
$sbrName="lib-br:convFssp2Daf";
return(0,"*** ERROR $sbrName: fileFssp=$fileFssp missing\n")
if (! defined $fileFssp || ! -e $fileFssp);
$dirDsspLoc="" if (! defined $dirDsspLoc || ! -d $dirDsspLoc);
# ------------------------------
# run via system call:
# ------------------------------
if ($exeConv=~/\.pl/){
system("$exeConv $fileFssp $dirDsspLoc >> $fileDafTmp") && Carp::confess( "cmd $exeConv $fileFssp $dirDsspLoc >> $fileDafTmp failed: ".( $? >> 8 ) ); }
# ------------------------------
# include as package
# ------------------------------
else {
&conv_fssp2daf_lh'conv_fssp2daf_lh($fileFssp,$dirDsspLoc,"fileOut=$fileDafTmp"); } # e.e'
# ------------------------------
# as Liisa cannot do it: clean up!
$fhinLoc= "FhInconvFssp2Daf"; $fhoutLoc="FhOutconvFssp2Daf";
&open_file("$fhinLoc","$fileDafTmp") ||
return(0,"*** ERROR $sbrName failed to open temp=$fileDafTmp (piped from $exeConv)\n");
&open_file("$fhoutLoc",">$fileDaf") ||
return(0,"*** ERROR $sbrName failed to open new=$fileDaf\n");
# ------------------------------
while(<$fhinLoc>){ # header
$tmp=$_;
last if (/^\# idSeq/);print $fhoutLoc $tmp; }
$tmp=~s/^\# //g; # correct error 1 (names)
$tmp=~s/\n//g;$tmp=~s/^[\t\s]*|[\t\s]*$//g;
@tmp=split(/[\t\s]+/,$tmp);
foreach $tmp(@tmp){
print $fhoutLoc "$tmp\t";}print $fhoutLoc "\n";
# ------------------------------
while(<$fhinLoc>){ # body
$_=~s/\n//g;$_=~s/^[\s\t]*|[\s\t]*$//g; # purge trailing blanks
@tmp=split(/[\t\s]+/,$_);
$seq=$tmp[$#tmp-1];$str=$tmp[$#tmp];
# consistency
return(0,"*** ERROR in $sbrName: lenSeq ne lenStr!\n".
"*** seq=$seq,\n","*** str=$str,\n","*** line=$_,\n")
if (length($seq) != length($str));
$seqOut=$strOut=""; # expand small caps
foreach $it (1..length($seq)){
$seq1=substr($seq,$it,1);$str1=substr($str,$it,1);
if ( ($seq1=~/[a-z]/) && ($str1=~/[a-z]/) ){
$seq1=~tr/[a-z]/[A-Z]/;$str1=~tr/[a-z]/[A-Z]/;$seqOut.=$seq1;$strOut.=$str1;}
elsif ($seq1=~/[a-z]/){
$seq1=~tr/[a-z]/[A-Z]/;$seqOut.=$seq1;$strOut.=".";}
elsif ($str1=~/[a-z]/){
$str1=~tr/[a-z]/[A-Z]/;$seqOut.=".";$strOut.=$str1;}
else {$seqOut.=$seq1;$strOut.=$str1;}}
# print
$tmp[$#tmp-1]=$seqOut;$tmp[$#tmp]=$strOut;
foreach $tmp(@tmp){print $fhoutLoc "$tmp\t";}print $fhoutLoc "\n";
} close($fhinLoc);close($fhoutLoc);
return(1,"ok $sbrName") if ( (-e $fileDaf) && (&isDaf($fileDaf)));
return(0,"*** ERROR $sbrName output $fileDaf missing or not DAF format\n");
} # end of convFssp2Daf
#==============================================================================
sub convGcg2fasta {
local($fileInLoc,$fileOutLoc,$fragLoc,$LshortNamesLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convGcg2fasta converts GCG to FASTA format
# in: $fileInLoc,$fileOutLoc,$fragLoc
# in: $fragLoc=n-m fragment to extract (optional)
# in: $LshortNamesLoc: if 1 names <=15 characters
# out: implicit: file out
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."convGcg2fasta";$fhinLoc="FHIN_"."convGcg2fasta";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
$fragLoc=0 if (! defined $fragLoc);
$LshortNamesLoc=0 if (! defined $LshortNamesLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# ------------------------------
($Lok,$id,$seq)= # read GCG
&gcgRd($fileInLoc);
return(0,"*** ERROR $sbrName: failed to read SWISS ($fileInLoc)\n".
"*** found id=$id\n")
if (! $Lok || length($seq)<1);
undef %tmp;
$tmp{"id","1"}= $id;
$tmp{"seq","1"}=$seq;
$tmp{"NROWS"}=1;
# ------------------------------
# extract?
if ($fragLoc){($beg,$end)=split(/-/,$frag);
foreach $it (1..$tmp{"NROWS"}){
$tmp{"seq",$it}=substr($tmp{"seq",$it},$beg,($end-$beg+1));}}
$ctres=length($tmp{"seq",1});
# ------------------------------
# shorten names?
# ------------------------------
if ($LshortNamesLoc){
undef %tmp2;
foreach $it (1..$tmp{"NROWS"}){
if (length($tmp{"id",$it})<=15) {
$tmp2{$tmp{"id",$it}}=1;
next;}
# too long
$id=$tmp{"id",$it};
$id=~s/^.*\|//g; # purge paths
# purge blanks
$id=~s/\s//g if (length($id)>15);
# purge extensions
$id=~s/\.[a-z]//g if (length($id)>15);
# cleave
if (length($id)>15){
$id=substr($id,1,15);}
# not unique
if (defined $tmp2{$id}){
$id=substr($id,1,12);
$ct=1;$idtmp=$id.$ct;
while(defined $tmp2{$idtmp}){
++$ct;
last if ($ct>999);}
$id=$idtmp;}
return(0,"*** $sbrName: shoot id=$id, orig=",,", failed shortening\n")
if (defined $tmp2{$id} || length($id)>15);
$tmp2{$id}=1;
$tmp{"id",$it}=$id;
}
undef %tmp2; }
# ------------------------------
# write output
($Lok,$msg)=
&fastaWrtMul($fileOutLoc,%tmp);
return(0,"*** ERROR $sbrName: failed to write FASTAmul ($fileOutLoc)\n".
"*** msg=$msg\n") if (! $Lok);
return(2,"-*- WARN $sbrName: wrong number written\n$msg\n") if ($Lok != 1);
return(1,"ok $sbrName");
} # end of convGcg2fasta
#==============================================================================
sub convHssp2seq {
local($fileInLoc,$chainInLoc,$fileOutLoc,$formOutLoc,$extOutLoc,
$doExpand,$fragLoc,$extrLoc,$lenMin,$laliMin,$distMin,$pideMax,$fhErrSbr,
$doSplitChainLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convHssp2seq converts HSSP file to PIR(mul), FASTA(mul)
# in: $fileInLoc file.hssp, file.out, format_of_output_file
# in: $fileOutLoc output file with converted sequence(s)
# in: $formOut output format (lower caps)
# = 'fasta|pir' (or pirmul/fastamul)
# in: $extOutLoc extension of expected output
# (fragments into _beg_end$extension)
# in: $doExpand do expand the deletions? (only for MSF)
# in: $frag fragment e.g. '1-5','10-100'
# = 0 for any
# NOTE: only ONE fragment allowed, here
# in: $extrIn number of protein(s) to extract
# = 'p1-p2,p3' -> extract proteins p1-p2,p3
# = 0 for all
# NOTE: = guide to write only the guide sequence!!
# in: $lenMin minimal length of sequence to write
# = 0 for any
# in: $laliMin minimal alignment length (0 for wild card)
# = 0 for any
# in: $distMin minimal distance from HSSP threshold
# = 0 for any
# in: $pideMAx !! maximal sequence identity
# = 0 for any
# in: $fhSbr ERRORs of convert_seq
# in: $doSplitChain split chains when converting to FASTA
#
# in GLOBAL $par{"pre_id"} -> id -> 'DB|id name'
#
# out: 1|0,msg,implicit: converted file
#
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="lib-br::"."convHssp2seq"; $fhinLoc="FHIN_"."convHssp2seq";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
$chainInLoc="*" if (! defined $chainInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOutLoc!") if (! defined $formOutLoc);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def doExpand!") if (! defined $doExpand);
return(0,"*** $sbrName: not def fragLoc!") if (! defined $fragLoc);
return(0,"*** $sbrName: not def extrLoc!") if (! defined $extrLoc);
$lenMin=0 if (! defined $lenMin);
$laliMin=0 if (! defined $laliMin);
$distMin=0 if (! defined $distMin);
$pideMax=0 if (! defined $pideMax);
$fhErrSbr="STDOUT" if (! defined $fhErrSbr);
$doSplitChainLoc=0 if (! defined $doSplitChainLoc);
# existence of file
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# ------------------------------
# supported output options
return(&errSbr("output format $formOutLoc not supported by this sbr"))
if ($formOutLoc !~ /^(pir|fasta)/);
# ------------------------------
if ($fragLoc) { # fragment of proteins
return(&errSbr("frag MUST be 'N1-N2', only ONE!")) if ($fragLoc !~/\d+\-\d+/);
($ifirFrag,$ilasFrag)=split(/\-/,$fragLoc); }
else {
$ifirFrag=$ilasFrag=0; }
$LextrGuideOnly=0; # ------------------------------
undef %extr; # extraction of proteins
if ($extrLoc eq "guide"){ # only guide
$LextrGuideOnly=1;}
elsif ($extrLoc) { # get numbers to extract
return(&errSbr("extr MUST be of the form:\n".
"'extr=n1-n2', or 'extr=n1,n2,n3-n4,n5'"))
if ($extr !~ /\d/);
@extr=&get_range($extr);
return(&errSbr("you gave the argument 'extr=$extr', not valid!\n".
"*** Ought to be of the form:\n".
"'extr=n1-n2', or 'extr=n1,n2,n3-n4,n5'\n")) if ($#extr==0);
foreach $tmp (@extr) {
if ($tmp=~/\D/){
return(&errSbr("you gave the argument 'extr=$extr', not valid!\n".
"*** Ought to be of the form:\n".
"'extr=n1-n2', or 'extr=n1,n2,n3-n4,n5'\n")); }
$extr{"$tmp"}=1; }}
# ------------------------------
# determine id
$pdbid= $fileInLoc;$pdbid=~s/^.*\/|\.hssp//g;
$pdbid.="_".$chainInLoc if ($chainInLoc ne "*");
undef %tmp; # ------------------------------
if ($chainInLoc ne "*"){ # get chain positions
($Lok,%tmp)=
&hsspGetChain($fileInLoc);
return(&errSbr("failed on getchain($fileInLoc)")) if (! $Lok);
foreach $it (1..$tmp{"NROWS"}){
next if ($chainInLoc ne $tmp{$it,"chain"});
$ifirChain=$tmp{$it,"ifir"}; $ilasChain=$tmp{$it,"ilas"}; }}
else {
$ifirChain=$ilasChain=0;}
# ------------------------------
undef %tmp; # read header of HSSP
($Lok,%tmp)=
&hsspRdHeader($fileInLoc,"HEADER","SEQLENGTH","ID","IDE","LALI","IFIR","ILAS");
return(&errSbr("failed on $fileInLoc")) if (! $Lok);
$header="";
$header=$tmp{"HEADER"} if (defined $tmp{"HEADER"});
# ------------------------------
# too short -> skip
return(1,"too short=".$tmp{"SEQLENGTH"}) if ($tmp{"SEQLENGTH"} < $lenMin);
$#numTake=0; # ------------------------------
# process data
if ($LextrGuideOnly){ # guide, only -> skip the following
push(@numTake,1);
$tmp{"NROWS"}=0; }
foreach $it (1..$tmp{"NROWS"}){ # loop over all alis
# not to include
next if ($extrLoc && ! defined $extr{$it});
# not chain -> skip
next if ($ifir && $ilas &&
( ($tmp{"IFIR",$it} > $ilas) || ($tmp{"ILAS",$it} < $ifir) ));
# lali too short
next if ($laliMin > $tmp{"LALI",$it} );
# pide too high
next if ($pideMax && $pideMax < 100*$tmp{"IDE",$it} );
# distance from threshold too high
if ($distMin){
# compile distance to HSSP threshold (new)
($pideCurve,$msg)=
&getDistanceNewCurveIde($tmp{"LALI",$it});
next if ($msg !~ /^ok/);
$dist=100*$tmp{"IDE",$it} - $pideCurve;
next if ($dist < $distMin); }
push(@numTake,$it); # ok -> take
}
# ------------------------------
undef %tmp; # read alignments
$kwdSeq="seqNoins"; # default: read ali without insertions
$kwdSeq="seqAli" if ($doExpand); # wanted: read ali with insertions
($Lok,%tmp)=
&hsspRdAli($fileInLoc,@numTake,$kwdSeq);
return(&errSbrMsg("failed reading alis for $fileInLoc, num=".
join(',',@numTake),$msg)) if (! $Lok);
$nali=$tmp{"NROWS"};
undef %tmp2;
# ------------------------------
if (defined $fragLoc){ # adjust for extraction (arg: frag=N1-n2)
# additional complication if expand: change numbers
if ($kwdSeq eq "seqAli"){
$seq=$tmp{$kwdSeq,"0"};
@tmp=split(//,$seq); $ct=0;
foreach $it (1..$#tmp){
next if ($tmp[$it] eq "."); # skip insertions
++$ct; # count no-insertions
next if ($ct > $ifirFrag); # outside of range to read
next if ($ct < $ilasFrag); # outside of range to read
$ifirFrag=$it if ($ct == $ifirFrag); # change begin !! WARN !!
$ilasFrag=$it if ($ct == $ilasFrag);}}} # change end !! WARN !!
# ----------------------------------------
# cut out non-chain, and not to read parts
# ----------------------------------------
foreach $it (0..$nali){
# guide, only -> skip the following
last if ($LextrGuideOnly && $it>0);
# chain restricts reading
if ($ifirChain && $ilasChain){
$tmp{$kwdSeq,$it}=
substr($tmp{$kwdSeq,$it},$ifirChain,($ilasChain-$ifirChain+1));}
# wanted fragment restricts reading
if ($ifirFrag && $ilasFrag){
$len=length($tmp{$kwdSeq,$it});
return(&errSbr(" : sequence outside (f=$fileInLoc, c=$chainInLoc)\n".
"itNali=$it, ifirFrag=$ifirFrag, len=$len, kwdSeq=$kwdSeq,\n".
"seq=".$tmp{$kwdSeq,$it}))
if ( $len < $ifirFrag);
$lenWrt=($ilasFrag-$ifirFrag+1);
$lenWrt=$len-$ifirFrag+1 if ($lenWrt < $len);
$tmp{$kwdSeq,$it}=
substr($tmp{$kwdSeq,$it},$ifirFrag,$len); }
$ct=$it+1;
$tmp2{"seq",$ct}=$tmp{$kwdSeq,$it};
undef $tmp{$kwdSeq,$it}; # slim-is-in !
$tmp2{"id",$ct}= $tmp{$it};
$tmp2{"id",$ct}.="_".$chainInLoc if ($ct==1 && $chainInLoc ne "*");
# add db asf
$tmp2{"id",$ct}=
$par{"pre_id"}."|".$tmp2{"id",$ct}." ".$header
if ($par{"pre_id"});
}
$tmp2{"NROWS"}=$nali+1;
$tmp2{"NROWS"}=1 if ($LextrGuideOnly);
undef %tmp; # slim-is-in!
# ------------------------------
undef %tmp; # slim-is-in !
undef @numTake; # slim-is-in !
# --------------------------------------------------
# write output file
# --------------------------------------------------
if ($formOutLoc =~ /^pir/){ # PIR, PIRmul
($Lok,$msg)=
&pirWrtMul($fileOutLoc,%tmp2); }
else { # FASTA, FASTAmul
($Lok,$msg)=
&fastaWrtMul($fileOutLoc,%tmp2); }
return(&errSbrMsg("failed writing out=$fileOutLoc, for in=$fileInLoc",$msg)) if (! $Lok);
print $fhErrSbr # warning if returned Lok==2
"-*- WARN $sbrName: outformat=$formOutLoc, not enough written:\n",$msg,"\n"
if ($Lok==2);
undef %tmp2; # slim-is-in !
return(1,"ok $sbrName");
} # end of convHssp2seq
#==============================================================================
sub convMsf2saf {
local($fileInLoc,$fileOutLoc,$doCompressLoc) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convMsf2saf converts MSF into SAF format
# in: fileMsf,fileSaf
# out: 0|1,$msg
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:convMsf2saf";$fhinLoc="FHIN_"."convMsf2saf";$fhoutLoc="FHOUT_"."convMsf2saf";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
$doCompressLoc=0 if (! defined $doCompressLoc ||
$doCompressLoc ne "1");
# --------------------------------------------------
# change br 2000-02: read and write & compress
# --------------------------------------------------
($Lok,$msg,%tmp)=
&msfRd($fileInLoc); return(0,"*** $sbrName: failed on msfRd msg=\n".
$msg) if (! $Lok);
return(0,"*** ERROR $sbrName: $fileInLoc no valid MSF file?\n")
if ($tmp{"NROWS"}==0);
# cleave off insertions in guide sequence
if ($doCompressLoc){
$lenloc=length($tmp{"seq",1});
$ctcleave=$ctres=0;
# all 0
foreach $itprot (1..$tmp{"NROWS"}){
$tmp{"new",$itprot}="";
}
# loop over all residues
foreach $itres (1..$lenloc){
# is residue
if (substr($tmp{"seq",1},$itres,1)=~/^[A-Za-z]/){
foreach $itprot (1..$tmp{"NROWS"}){
$tmp{"new",$itprot}.=substr($tmp{"seq",$itprot},$itres,1);
}
++$ctres;
next;}
# seems insertion
++$ctcleave;
}
# check: sum ok?
return(0,"*** $sbrName: failed at compressing ncleave=$ctcleave, nresnew=$ctres,".
" before=".$lenloc." file=$fileInLoc!")
if ($lenloc != ($ctcleave + $ctres));
# replace by cleaved version
foreach $itprot (1..$tmp{"NROWS"}){
$tmp{"seq",$itprot}=$tmp{"new",$itprot};
}
}
# ------------------------------
# now write SAF
# ------------------------------
($Lok,$msg)=
&safWrt($fileOutLoc,
%tmp); return(0,"*** $sbrName: failed writing SAF=$fileOutLoc, in=".
$fileInLoc." err msg=\n".$msg) if (! $Lok);
return(0,"*** $sbrName: failed writing SAF=$fileOutLoc, in=".
$fileInLoc) if ( ! -e $fileOutLoc);
undef %tmp; # slim-is-in
return(1,"ok $sbrName");
# **************************************************
# dead code before 2000-02
open($fhinLoc,$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) ||
return(0,"*** ERROR $sbrName: fileIn=$fileInLoc, not opened\n");
$#tmp=$ct=$Lname=$LMsf=$LSeq=0;
# ------------------------------
while (<$fhinLoc>) { # read MSF file
$_=~s/\n//g;
# --------------------
# find sequence
if (! $LSeq && $_=~/^\/\// && $Lname && $LMsf){
$LSeq=1;}
# --------------------
elsif (! $LSeq){ # header
$LMsf=1 if (! $LMsf && $_=~/msf\s*of\s*\:|msf\:\s+\d+/i);
$Lname=1 if (! $Lname && $_=~/name\s*:/i);
push(@tmp,$_) if (! $Lname); } # store header
# --------------------
elsif ($LSeq){ # sequence
# first open file
if ($ct==0){
open($fhoutLoc,">".$fileOutLoc) || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(0,"*** ERROR $sbrName: failed opening fileout (saf)=$fileOutLoc\n");
print $fhoutLoc "# SAF (Simple Alignment Format)\n";
foreach $tmp(@tmp){
print $fhoutLoc "# $tmp\n";
}
}
++$ct;
print $fhoutLoc "$_\n"; # simply mirror file
}
}
close($fhinLoc); close($fhoutLoc) if ($ct>0);
$#tmp=0; # save memory
return(0,"*** ERROR $sbrName: $fileInLoc no valid MSF file\n") if ($ct==0);
return(1,"ok $sbrName");
} # end of convMsf2saf
#==============================================================================
sub convPdb2seq {
local($fileInLoc,$chainInLoc,$fileOutLoc,$formOutLoc,$frag,$fhTraceLoc)=@_;
local($outformat,$an,$commandLoc);
#----------------------------------------------------------------------
# convPdb2seq convert PDB to sequence only
# in: $fileIn,$fileOut,$formOutLoc,$frag,$fhTraceLoc
# in: $chainInLoc= PDB chain
# = "*" for any
# in: $formOutLoc= 'FASTA|GCG|PIR'
# in: $frag= 1-5, fragment from 1 -5
# out: file
# err: ok=(1,'ok'), err=(0,'msg')
#----------------------------------------------------------------------
$sbrName="convPdb2seq";
$allow="fasta|pir|gcg";
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def chainInLoc!") if (! defined $chainInLoc);
$chainInLoc="*" if (length($chainInLoc) < 1 || $chainInLoc =~/\s/);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOutLoc!") if (! defined $formOutLoc);
$frag=0 if (! defined $frag);
$fhTraceLoc="STDOUT" if (! defined $fhTraceLoc);
# check existence of files
return(0,"*** $sbrName: no file '$fileInLoc'!") if (! -e $fileInLoc);
# check format
$formOutLoc=~tr/[A-Z]/[a-z]/;
return(0,"*** $sbrName: output format $formOutLoc not supported\n")
if ($formOutLoc !~ /$allow/);
$anFormOut=substr($formOutLoc,1,1);$anFormOut=~tr/[a-z]/[A-Z]/;
$frag=0 if ($frag !~ /\-/);
# ------------------------------
if ($frag){ # extract fragments?
$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
$frag=0 if ($beg =~/\D/ || $end =~ /\D/);}
# ------------------------------
# read PDB
($Lok,$msg,$rh_pdb)=
&pdbExtrSequence($fileInLoc,$chainInLoc,1);
return(0,"*** $sbrName: error in reading PDB $fileInLoc :\n".$msg."\n")
if (! $Lok);
return(2,"*** $sbrName: $fileInLoc is RNA DNA?\n")
if ($Lok==2);
return(0,"*** $sbrName: error in reading PDB $fileInLoc (not defined pdb(chains)):\n".
$msg."\n")
if (! defined $rh_pdb->{"chains"});
@chainTmp=split(/,/,$rh_pdb->{"chains"});
# ------------------------------
# loop over all chains
# ------------------------------
$seq=$chain="";
$name=0;
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g;
foreach $chainTmp (@chainTmp) {
$chain.=$chainTmp if ($chainTmp ne "none");
# ------------------------------
# id
# first line: id
if (! $name) {
$name=$id;
$name.=" ".$rh_pdb->{"header"} if (defined $rh_pdb->{"header"});
$name.=" ".$rh_pdb->{"compnd"} if (defined $rh_pdb->{"compnd"});
$name.=" source=".$rh_pdb->{"source"} if (defined $rh_pdb->{"source"});}
# ------------------------------
# next lines: sequence
$seqRd=$rh_pdb->{$chainTmp};
$seqRd=~s/\s//g;
# add '!' as chain symbol
$seq.="!" if (length($seq)>0);
$seq.=$seqRd; }
# ******************************
# not really found
return(0,"*** $sbrName: seq=$seq, for file=$fileInLoc,$chainInLoc,$frag!")
if (length($seq)<1);
# ******************************
# add all chains to name
$name.=" chains=".join(',',split(//,$chain)) if (length($chain)>0);
# ------------------------------
# extract fragment
if ($frag) {
return(0,"*** ERROR $sbrName: $fileInLoc seqrd=".
$seq."*** however wanted to restrict to fragment from $beg-$end\n")
if (length($seq)<$beg);
$seq=substr($seq,$beg);
$lenWant=1+$end-$beg;
if (length($seq)<$lenWant) {
print $fhTraceLoc
"-*- WARN $sbrName: $fileInLoc ($chainTmp) shorter than expected!\n",
"-*- wanted $beg-$end, but is ",length($seq)," residues long\n"; }
else {
$seq=substr($seq,1,$lenWant);}}
# ------------------------------
# write out
$Lok=0;
if ($formOutLoc =~ /^pir/){
($Lok,$msg)=&pirWrtOne($fileOutLoc,$id,$seq); }
elsif ($formOutLoc =~ /^fasta/){
($Lok,$msg)=&fastaWrt($fileOutLoc,$id,$seq); }
elsif ($formOutLoc =~ /^gcg/){
($Lok,$msg)=&gcgWrt($fileOutLoc,$id,$seq); }
#
return(0,"*** $sbrName: error in converting PDB $fileInLoc:\n".$msg."\n")
if (! $Lok);
return(1,"ok $sbrName");
} # end of convPdb2seq
#===============================================================================
sub convPhd2dssp {
local($fileInLoc,$fileOutLoc,$chainLoc,$fhErrSbr) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convPhd2dssp converts PHDrdb format to DSSP format
# in: $fileInLoc,$fileOutLoc,$chainLoc,
# in: $chainLoc chain name ([A-Z0-9 ])
# in: $fhErrSbr 0 for no write
# out: 1|0,msg, implicit: writes fileDSsp
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."convPhd2dssp";
$fhinLoc="FHIN_"."convPhd2dssp";$fhoutLoc="FHOUT_"."convPhd2dssp";
# ------------------------------
# check arguments
return(&errSbr("not def fileInLoc!")) if (! defined $fileInLoc);
return(&errSbr("not def fileOutLoc!")) if (! defined $fileOutLoc);
$chainLoc=" " if (! defined $chainLoc);
$fhErrSbr="STDOUT" if (! defined $fhErrSbr);
# return(&errSbr("not def !")) if (! defined $);
# return(&errSbr("not def !")) if (! defined $);
return(&errSbr("no fileIn=$fileInLoc!")) if (! -e $fileInLoc);
# ------------------------------
# defaults
# keywords to read from RDB file
@kwdLoc =("No","AA","PHEL","RI_S","PACC","RI_A");
$idLoc=$fileInLoc;
$idLoc=~s/^.*\///g;$idLoc=~s/\s|\n|\.rdb.*//g;
# --------------------------------------------------
# read RDB file
# --------------------------------------------------
undef %rd;
%rd=
&rdRdbAssociative($fileInLoc,"body",@kwdLoc);
# --------------------------------------------------
# store into NUM, SEQ, SEC, RISEC, ACC, RIACC
# --------------------------------------------------
$#NUM=$#SEQ=$#SEC=$#RISEC=$#ACC=$#RIACC=0;
foreach $kwd (@kwdLoc) {
next if (! defined $rd{$kwd,"1"}) ;
if ($kwd eq "No") {
$ct=1; while(defined $rd{$kwd,$ct}){push(@NUM,$rd{$kwd,$ct});++$ct;}}
elsif ($kwd eq "AA") {
$ct=1; while(defined $rd{$kwd,$ct}){push(@SEQ,$rd{$kwd,$ct});++$ct;}}
elsif ($kwd eq "PHEL") {
$ct=1; while(defined $rd{$kwd,$ct}){push(@SEC,$rd{$kwd,$ct});++$ct;}}
elsif ($kwd eq "RI_S") {
$ct=1; while(defined $rd{$kwd,$ct}){push(@RISEC,$rd{$kwd,$ct});++$ct;}}
elsif ($kwd eq "PACC") {
$ct=1; while(defined $rd{$kwd,$ct}){push(@ACC,$rd{$kwd,$ct});++$ct;}}
elsif ($kwd eq "RI_A") {
$ct=1; while(defined $rd{$kwd,$ct}){push(@RIACC,$rd{$kwd,$ct});++$ct;}}
}
# ------------------------------
# convert L->' '
foreach $it(1..$#SEC){
$SEC[$it]=~s/L/ /;}
# --------------------------------------------------
# writing phd into DSSP format
# --------------------------------------------------
$CHAIN=$chainLoc;
print $fhErrSbr
"--- $sbrName: writing id=$idLoc, chain=$CHAIN, fileOut=$fileOutLoc\n"
if ($fhErrSbr);
# NOTE: GLOBAL in: all $CHAIN,@NUM,@SEQ,@SEC,@ACC,@RI*
($Lok,$msg)=
&dsspWrtFromPhd($fileOutLoc,$idLoc);
if (! $Lok) { $msgErr="*** ERROR $scrName: failed writing $fileOutLoc\n".$msg;
Carp::confess( $msgErr ); }
$#NUM=$#SEQ=$#SEC=$#RISEC=$#ACC=$#RIACC=0; # slim-is-in!
undef %rd; # slim-is-in!
return(1,"ok $sbrName");
} # end of convPhd2dssp
#===============================================================================
sub convPhd2seq {
local($fileInLoc,$fileOutLoc,$formatOutLoc,$fhErrSbr) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convPhd2seq converts PHDrdb to SEQUENCE format || string
# in: $fileIn PHD rdb file
# in: $fileOut name of output file
# note: string returned if =0 !
# in: $formOut PIR|GCG|FASTA|keyword
# note: keyword determines which string is
# to be extracted:
# combine many by 'AA,PHEL,..'
# AA sequence
# OHEL observed sec str
# OHL observed HTM
# OACC observed accessibility (angstrom)
# OREL observed relative acc
#
# PHEL predicted sec str
# PHL predicted HTM
# PFHL filtered HTM
# PRHL refined HTM
# PiTo topology HTM
# PACC predicted accessibility (angstrom)
# PREL predicted relative acc
# Pbie predicted accessibility in 3 states
#
# RI_S reliability index sec str
# RI_A reliability index accessibility
# RI_H reliability index HTM
#
# pH normalised output unit H
# pE normalised output unit E
# pL normalised output unit L
# pb normalised output unit b (buried)
# pe normalised output unit e (exposed)
#
# OtH full output unit (0-100) H
# OtE full output unit (0-100) E
# OtL full output unit (0-100) L
# Otb full output unit (0-100) b (buried)
# Ote full output unit (0-100) e (exposed)
#
#
# out: $string1,$string2, or implicit file!
# NOTE: string1=that matching formatOut1
# NOTE2: residues separated by commata!
# err: (1,'ok',@strings), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."convPhd2seq";
$fhinLoc="FHIN_"."convPhd2seq";$fhoutLoc="FHOUT_"."convPhd2seq";
# ------------------------------
# check arguments
return(&errSbr("not def fileInLoc!")) if (! defined $fileInLoc);
return(&errSbr("not def fileOutLoc!")) if (! defined $fileOutLoc);
return(&errSbr("not def formatOutLoc!")) if (! defined $formatOutLoc);
$fhErrSbr="STDOUT" if (! defined $fhErrSbr);
# return(&errSbr("not def !")) if (! defined $);
return(&errSbr("no fileIn=$fileInLoc!")) if (! -e $fileInLoc);
# ------------------------------
# defaults
# keywords to read from RDB file
$#kwdLoc=0;
undef %translate;
if ($formatOutLoc =~/^(PIR|FASTA|GCG)$/i) {
push(@kwdLoc,"AA");}
elsif ($formatOutLoc) {
$formatOutLoc=~s/\s//g;
push(@kwdLoc,split(/,/,$formatOutLoc)); }
# --------------------------------------------------
# read RDB file
# --------------------------------------------------
undef %rd;
%rd=
&rdRdbAssociative($fileInLoc,"body",@kwdLoc);
# --------------------------------------------------
# extract strings (residues separated by commata)
# --------------------------------------------------
$#tmp=0;
foreach $kwd (@kwdLoc) {
next if (! defined $rd{$kwd,"1"});
$string="";
$it=1;
while (defined $rd{$kwd,$it}) {
$string.=$rd{$kwd,$it}.",";
++$it; }
$string=~s/\,$//g; # purge final comma
push(@tmp,$string); }
undef %rd; # slim-is-in
# ==================================================
# <--- <--- <--- <--- <--- <---
# EARLY end: just return strings
return(1,"ok",@tmp)
if (! $fileOutLoc || $formatOutLoc !~ /^(PIR|FASTA|GCG)$/i);
# <--- <--- <--- <--- <--- <---
# ==================================================
# --------------------------------------------------
# writing phd into sequence file format
# --------------------------------------------------
$idLoc=$fileInLoc;$idLoc=~s/^.*\///g;
print $fhErrSbr
"--- $sbrName: writing id=$idLoc, fileOut=$fileOutLoc\n"
if ($fhErrSbr);
# output PIR format
if ($formatOutLoc =~/^pir/) { #
foreach $it (1..$#kwdLoc) {
next if ($kwdLoc[$it] !~/^AA$/);
$seq=$tmp[$it];
$seq=~s/\,//g; # purge commata
last; }
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g;
($Lok,$msg)=
&pirWrtOne($fileOutLoc,$id,$seq);
return(0,"*** ERROR $sbrName: failed converting PHDrdb to PIR\n".$msg)
if (! $Lok); }
# output FASTA format
elsif ($formatOutLoc =~/^fasta/) {
foreach $it (1..$#kwdLoc) {
next if ($kwdLoc[$it] !~/^AA$/);
$seq=$tmp[$it];
$seq=~s/\,//g; # purge commata
last; }
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g;
($Lok,$msg)=
&fastaWrt($fileOutLoc,$id,$seq);
return(0,"*** ERROR $sbrName: failed converting PHDrdb to FASTA\n")
if (! $Lok);}
# output format unknown
else {
return(0,"*** ERROR $sbrName: output format $formatOutLoc unknown!\n");
}
$#tmp=0; # slim-is-in!
$#kwdLoc=0; # slim-is-in!
return(1,"ok $sbrName");
} # end of convPhd2seq
#===============================================================================
sub convPhdGen {
local($fileInLoc,$chainInLoc,$fileOutLoc,$formIn,$formOut,$extOutLoc,
$frag,$fileScreenLoc,$dirWork,$fhSbr) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convPhdGen general converter for PHD predictions into -> x
# in: for general info see 'convPhdGen'
# out: converted file
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convPhdGen";$fhinLoc="FHIN"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def chainInLoc!") if (! defined $chainInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formIn!") if (! defined $formIn);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def frag!") if (! defined $frag);
return(0,"*** $sbrName: not def fileScreenLoc!") if (! defined $fileScreenLoc);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
$chainIn=$chainInLoc; $chainIn="*"
if (! $chainInLoc || length($chainInLoc)!=1 || $chainInLoc !~/[A-Z0-9]/);
$#beg=$#end=0;
# ------------------------------
if ($frag && # extract fragments? NOT for DSSP!
($formOut eq "dssp" || $formOut =~ /^(pir|fasta)/)){
print "-*- WARN $sbrName: fragments not supported for PHD-><DSSP|PIR|FASTA>\n";
$frag=0; }
# ------------------------------
if ($frag){ # extract fragments?
@tmp=split(/,/,$frag);$#beg=$#end=0;
foreach $frag(@tmp){next if ($frag !~ /\-/);$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
next if ($beg =~/\D/ || $end =~ /\D/);
push(@beg,$beg);push(@end,$end);}}
# ------------------------------
# DSSP out
if ($formOut eq "dssp") {
($Lok,$msg)=
&convPhd2dssp($fileInLoc,$fileOutLoc,$chainLoc,$fhSbr);
return(0,"*** ERROR $sbrName: failed to convert PHDrdb to $formOut\n".
$msg."\n") if (! $Lok);
push(@fileOut,$fileOutLoc); }
# ------------------------------
# convert to sequence formats
elsif ($formOut =~ /^(pir|fasta)/){
($Lok,$msg)=
&convPhd2seq($fileInLoc,$fileOutLoc,$formOut,$fhSbr);
return(0,"*** ERROR $sbrName: failed to convert PHDrdb to $formOut\n".
$msg."\n") if (! $Lok);
push(@fileOut,$fileOutLoc);}
# ------------------------------
# convert to HTML
elsif ($formOut eq "html"){
print "xx html : working on it !\n";
Carp::confess("*** output format is HTML??? not yet in it!");
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
($Lok,$id,$seq)=&fastaRdGuide($fileInLoc);
$tmp{"seq","1"}=substr($seq,$beg[$it],($end[$it]-$beg[$it]+1));
$tmp{"NROWS"}= 1;$tmp{"id","1"}= $id;
($Lok,$msg)=&safWrt($fileOutTmp,%tmp);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutTmp);}}
else {$fragHere=0;
($Lok,$id,$tmp{"seq","1"})=
&fastaRdGuide($fileInLoc);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
$id=~s/^(\S+).*$/$1/;
$tmp{"NROWS"}= 1;$tmp{"id","1"}= $id;
($Lok,$msg)=&safWrt($fileOutLoc,%tmp);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutLoc);}}
else {
return(2,"*** ERROR $sbrName: output option $formOut not supported for $formIn\n");}
return(1,"ok $sbrName");
} # end of convPhdGen
#==============================================================================
sub convPir2fasta {
local($fileInLoc,$fileOutLoc,$fragLoc,$extrLoc,$LshortNamesLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convPir2fasta converts PIR to FASTA format
# in: $fileInLoc,$fileOutLoc,$fragLoc,$extrLoc
# in: $fragLoc=n-m fragment to extract (optional)
# in: $extrLoc=i,j,k take only sequences i,j,k from PIRmul
# NOTE: to leave blank =0, e.g.
# 'file.pir,file.f,0,5' would get fifth sequence
# in: $LshortNamesLoc: if 1 names <=15 characters
# out: implicit: file out
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."convPir2fasta";$fhinLoc="FHIN_"."convPir2fasta";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
$fragLoc=0 if (! defined $fragLoc);
$extrLoc=0 if (! defined $extrLoc);
$LshortNamesLoc=0 if (! defined $LshortNamesLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# interpret input
$num=$extrLoc;# $num=1 if (! $extrLoc);
# ------------------------------
($Lok,$id,$seq)= # read PIR
&pirRdMul($fileInLoc,$num);
return(0,"*** ERROR $sbrName: failed to read PIRmul ($fileInLoc,$num)\n".
"*** found id=$id\n")
if (! $Lok || length($seq)<1);
# ------------------------------
# interpret info
@id=split(/\n/,$id);@seq=split(/\n/,$seq);
return(0,"*** ERROR $sbrName: seq=$seq, and id=$id, not matching (differing number)\n")
if ($#id != $#seq);
$tmp{"NROWS"}=$#id;
foreach $it (1..$#id){$tmp{"id",$it}= $id[$it];
$tmp{"seq",$it}=$seq[$it];}
# ------------------------------
# extract?
if ($fragLoc){($beg,$end)=split(/-/,$frag);
foreach $it (1..$tmp{"NROWS"}){
$tmp{"seq",$it}=substr($tmp{"seq",$it},$beg,($end-$beg+1));}}
$ctres=length($tmp{"seq",1});
# ------------------------------
# shorten names?
if ($LshortNamesLoc){
undef %tmp2;
foreach $it (1..$tmp{"NROWS"}){
if (length($tmp{"id",$it})<=15) {
$tmp2{$tmp{"id",$it}}=1;
next;}
# too long
$id=$tmp{"id",$it};
$id=~s/^.*\|//g; # purge paths
# purge blanks
$id=~s/\s//g if (length($id)>15);
# purge extensions
$id=~s/\.[a-z]//g if (length($id)>15);
# cleave
if (length($id)>15){
$id=substr($id,1,15);}
# not unique
if (defined $tmp2{$id}){
$id=substr($id,1,12);
$ct=1;$idtmp=$id.$ct;
while(defined $tmp2{$idtmp}){
++$ct;
last if ($ct>999);}
$id=$idtmp;}
return(0,"*** $sbrName: shoot id=$id, orig=",,", failed shortening\n")
if (defined $tmp2{$id} || length($id)>15);
$tmp2{$id}=1;
$tmp{"id",$it}=$id;
}
undef %tmp2; }
# ------------------------------
# write output
($Lok,$msg)=
&fastaWrtMul($fileOutLoc,%tmp);
return(0,"*** ERROR $sbrName: failed to write FASTAmul ($fileOutLoc)\n".
"*** msg=$msg\n") if (! $Lok);
return(2,"-*- WARN $sbrName: wrong number written\n$msg\n") if ($Lok != 1);
return(1,"ok $sbrName");
} # end of convPir2fasta
#==============================================================================
sub convSaf2many {
local($fileInLoc,$fileOutLoc,$formOutLoc,$fragLoc,$extrLoc,$fhErrSbr,
$LdoCompressLoc,$LshortNamesLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convSaf2many converts SAF into many formats: saf2msf, saf2fasta, saf2pir
# in: $fileInLoc,$fileOutLoc,$formOutLoc,$fragLoc,$extrLoc,$fhErrSbr
# in: $formOutLoc format MSF|FASTA|PIR
# in: $fragLoc=n-m fragment to extract (optional)
# in: $extrLoc=i,j,k take only sequences i,j,k from PIRmul
# in: NOTE: to leave blank =0, e.g.
# in: 'file.saf,file.f,0,5' would get fifth sequence
# in: $LdoCompressLoc delete insertions in master
# in: $LshortNamesLoc: if 1 names <=15 characters
# out: implicit: file written
# err: (1,'ok'), (0,'message')
# err: e: (1,msg) -> ok
# err: a: (0,msg) -> some arguments missing/files not opened
# err: b: (2,msg) -> no output file written
# err: b: (3,msg) -> ERROR from msfCheckFormat
# specification of format see interpretSeqSaf
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."convSaf2many";$fhinLoc="FHIN_"."convSaf2many";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOutLoc!") if (! defined $formOutLoc);
$fragLoc=0 if (! defined $fragLoc);
$extrLoc=0 if (! defined $extrLoc);
$LdoCompressLoc=0 if (! defined $LdoCompressLoc);
$LshortNamesLoc=0 if (! defined $LshortNamesLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# interpret input
$formOutLoc=~tr/[A-Z]/[a-z]/;
if ($fragLoc){$fragLoc=~s/\s//g;
return(0,"*** $sbrName: syntax of fragLoc ($fragLoc) must be :\n".
" 'ifir-ilas', where ifir,ilas are integers (or 1-*)\n")
if ($fragLoc && $fragLoc !~/[\d\*]\-[\d\*]/);}
if ($extrLoc){$extrLoc=~s/\s//g;
return(0,"*** $sbrName: syntax of extrLoc ($extrLoc) must be :\n".
" 'n1,n2,n3-n4', where n* are integers\n")
if ($extrLoc && $extrLoc =~/[^0-9\-,]/);
@extr=&get_range($extrLoc);
undef %take;
foreach $it(@extr){
$take{$it}=1;}}
# ------------------------------
# read file
($Lok,$msg,%safIn)=
&safRd($fileInLoc);
@nameLoc=split(/,/o,$safIn{"names"});
# ------------------------------
undef %tmp; $ctTake=0; # store names for passing variables
foreach $it (1..$#nameLoc){
next if ($extrLoc && (! defined $take{$it} || ! $take{$it}));
++$ctTake;
$tmp{"id",$ctTake}= $nameLoc[$it];
$tmp{"seq",$ctTake}=$safIn{"seq",$it};
}
$tmp{"NROWS"}=$ctTake;
%safIn=%tmp; undef %tmp;
# ------------------------------
# compress
# ------------------------------
if ($LdoCompressLoc){
$ctcleave=$ctres=0;
$lenloc=length($safIn{"seq",1});
# all 0
foreach $itprot (1..$safIn{"NROWS"}){
$safIn{"new",$itprot}="";
}
# loop over all residues
foreach $itres (1..$lenloc){
# is residue
if (substr($safIn{"seq",1},$itres,1)=~/^[A-Za-z]/){
foreach $itprot (1..$safIn{"NROWS"}){
$safIn{"new",$itprot}.=substr($safIn{"seq",$itprot},$itres,1);
}
++$ctres;
next;}
# seems insertion
++$ctcleave;
}
# check: sum ok?
return(0,"*** $sbrName: failed at compressing ncleave=$ctcleave, nresnew=$ctres,".
" before=".$lenloc." file=$fileInLoc!")
if ($lenloc != ($ctcleave + $ctres));
# replace by cleaved version
foreach $itprot (1..$safIn{"NROWS"}){
$safIn{"seq",$itprot}=$safIn{"new",$itprot};
}}
$ctres=length($safIn{"seq",1});
# ------------------------------
# select subsets
# ------------------------------
if ($fragLoc){
($beg,$end)=split("-",$fragLoc);$name=$safIn{"1"};$len=length($safIn{$name});
$beg=1 if ($beg eq "*"); $end=$len if ($end eq "*");
if ($len < ($end-$beg+1)){
print "-*- WARN $sbrName: $beg-$end not possible, as length of protein=$len\n";}
else {
foreach $it (1..$safIn{"NROWS"}){
$name=$safIn{"id",$it};
$safIn{"seq",$it}=substr($safIn{"seq",$it},$beg,($end-$beg+1));
}
}}
# ------------------------------
# shorten names?
# ------------------------------
if ($LshortNamesLoc){
undef %safIn2;
foreach $it (1..$safIn{"NROWS"}){
if (length($safIn{"id",$it})<=15) {
$safIn2{$safIn{"id",$it}}=1;
next;}
# too long
$id=$safIn{"id",$it};
$id=~s/^.*\|//g; # purge paths
# purge blanks
$id=~s/\s//g if (length($id)>15);
# purge extensions
$id=~s/\.[a-z]//g if (length($id)>15);
# cleave
if (length($id)>15){
$id=substr($id,1,15);}
# not unique
if (defined $safIn2{$id}){
$id=substr($id,1,12);
$ct=1;$idsafIn=$id.$ct;
while(defined $safIn2{$idsafIn}){
++$ct;
last if ($ct>999);}
$id=$idsafIn;}
return(0,"*** $sbrName: shoot id=$id, orig=",,", failed shortening\n")
if (defined $safIn2{$id} || length($id)>15);
$safIn2{$id}=1;
$safIn{"id",$it}=$id;
}
undef %safIn2; }
# --------------------------------------------------
# write output
# --------------------------------------------------
# write an MSF formatted file
if ($formOutLoc eq "msf"){
# reconvert to what MSF wants...
foreach $it (1..$safIn{"NROWS"}){$name=$safIn{"id",$it};
$tmp{$it}=$name;
$tmp{SEQS}->{$name}=$safIn{"seq",$it};}
$tmp{"NROWS"}=$safIn{"NROWS"};
$tmp{"FROM"}= $fileInLoc;
$tmp{"TO"}= $fileOutLoc;
$fhout="FHOUT_MSF_FROM_SAF";
open("$fhout",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) || # open file
return(0,"*** $sbrName cannot open fileOutLoc=$fileOutLoc\n");
$Lok=&msfWrt("$fhout",%tmp); # write the file
close("$fhout"); undef %tmp;}
# write a FASTA or PIR formatted file
elsif ($formOutLoc eq "fasta" || $formOutLoc eq "fastamul" || $formOutLoc eq "saf" ||
$formOutLoc eq "pirmul" || $formOutLoc eq "pir" || $formOutLoc eq "gcg"){
if ($formOutLoc =~ /^fasta/){
($Lok,$msg)=&fastaWrtMul($fileOutLoc,%safIn);}
elsif ($formOutLoc =~ /^pir/){
($Lok,$msg)=&pirWrtMul($fileOutLoc,%safIn);}
elsif ($formOutLoc eq "saf"){
($Lok,$msg)=&safWrt($fileOutLoc,%safIn);}
elsif ($formOutLoc eq "gcg"){
($Lok,$msg)=&gcgWrt($fileOutLoc,$safIn{"id","1"},$safIn{"seq","1"});}
return(0,"*** ERROR $sbrName: failed in $formOutLoc ($fileOutLoc)\n".$msg."\n")
if (! $Lok);}
else {
return(0,"*** $sbrName: output format $formOutLoc not supported\n");}
# ------------------------------
# file existing??
return(2,"*** $sbrName ERROR after write, missing fileOutLoc=$fileOutLoc\n")
if (! -e $fileOutLoc);
# ------------------------------
# make a basic test of msf format
if ($formOutLoc eq "msf"){
($Lok,$msg)=
&msfCheckFormat($fileOutLoc);
return(3,"$msg"."*** $sbrName ERROR from msfCheckFormat fileOutLoc=$fileOutLoc\n") if (! $Lok);}
# ------------------------------
$#safIn=$#nameLoc=0; # save space
undef %safIn; undef %nameInBlock; undef %tmp;
return(1,"$sbrName ok");
} # end of convSaf2many
#==============================================================================
sub convSeq2fastaPerl {
local($fileInLoc,$fileOutLoc,$formInLoc,$fragLoc,$LshortNamesLoc)=@_;
local($outformat,$an,$commandLoc);
#----------------------------------------------------------------------
# convSeq2fastaPerl convert all formats to fasta (no fortran)
# in: $fileInLoc,$fileOutLoc,$formInLoc,$fragLoc
# in: $formInLoc: pir, pirmul, gcg, swiss, dssp
# in: $fragLoce = 1-5, fragment from 1 -5
# in: $LshortNamesLoc: if 1 names <=15 characters
# out:
# err: ok=(1,'ok'), err=(0,'msg')
#----------------------------------------------------------------------
$sbrName="lib-br:convSeq2fastaPerl";
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formInLoc!") if (! defined $formInLoc);
$fragLoc=0 if (! defined $fragLoc);
$LshortNamesLoc=0 if (! defined $LshortNamesLoc);
# check existence of files
return(0,"*** $sbrName: no file '$fileInLoc'!") if (! -e $fileInLoc);
$fragLoc=0 if ($fragLoc !~ /\-/);
# ------------------------------
# do conversion
# ------------------------------
if ($formInLoc=~ /^pir/){ # PIR
($Lok,$msg)=
&convPir2fasta($fileInLoc,$fileOutLoc,$fragLoc,$LshortNamesLoc);}
elsif ($formInLoc=~ /^swiss/){ # SWISS-PROT
($Lok,$msg)=
&convSwiss2fasta($fileInLoc,$fileOutLoc,$fragLoc,$LshortNamesLoc);}
elsif ($formInLoc eq "gcg"){ # GCG
($Lok,$msg)=
&convGcg2fasta($fileInLoc,$fileOutLoc,$fragLoc,$LshortNamesLoc);}
else {
return(&errSbr("format $formInLoc to FASTA not supported"));}
return(&errSbrMsg("failed converting format=$formInLoc ($fileInLoc,$fileOutLoc,$fragLoc)",
$msg)) if (! $Lok);
return(1,"ok $sbrName");
} # end of convSeq2fastaPerl
#==============================================================================
sub convSeq2seq {
local($fileInLoc,$formInLoc,$fileOutLoc,$formOutLoc,$frag,$fileScreenLoc,$fhTraceLoc)=@_;
local($outformat,$an,$commandLoc);
#----------------------------------------------------------------------
# convSeq2seq convert all sequence-only formats to sequence only
# in: $exeConvSeq,$fileIn,$fileOut,$formOutLoc,$frag,$fileScreen,$fhTraceLoc
# in: $formOutLoc= 'FASTA|GCG|PIR'
# in: $frage = 1-5, fragment from 1 -5
# out: file
# err: ok=(1,'ok'), err=(0,'msg')
#----------------------------------------------------------------------
$sbrName="lib-br:convSeq2seq";
$allow="fasta|pir|gcg";
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def formInLoc!") if (! defined $formInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOutLoc!") if (! defined $formOutLoc);
$fileScreenLoc=0 if (! defined $fileScreenLoc);
$frag=0 if (! defined $frag);
$fhTraceLoc="STDOUT" if (! defined $fhTraceLoc);
# check existence of files
return(0,"*** $sbrName: no file '$fileInLoc'!") if (! -e $fileInLoc);
# check format
$formInLoc=~tr/[A-Z]/[a-z]/;
$formOutLoc=~tr/[A-Z]/[a-z]/;
return(0,"*** $sbrName: output format $formOutLoc not supported\n")
if ($formOutLoc !~ /$allow/);
$anFormOut=substr($formOutLoc,1,1);$anFormOut=~tr/[a-z]/[A-Z]/;
$frag=0 if ($frag !~ /\-/);
# ------------------------------
# get input
$Lok=$id=0;
if ($formInLoc =~/swiss/) { ($Lok,$id,$seq)=&swissRdSeq($fileInLoc); }
elsif ($formInLoc =~/fasta/) { ($Lok,$id,$seq)=&fastaRdMul($fileInLoc,1); }
elsif ($formInLoc =~/pir/) { ($Lok,$id,$seq)=&pirRdMul($fileInLoc,1); }
elsif ($formInLoc =~/gcg/) { ($Lok,$id,$seq)=&gcgRdMul($fileInLoc); }
return(&errSbrMsg("input format=$formInLoc, not valid!\n"))
if (! $Lok && ! $id);
return(&errSbrMsg("problem reading input format=$formInLoc, file=$fileInLoc!\n"))
if (! $Lok);
# ------------------------------
if ($frag){ # extract fragments?
$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
if ($beg =~/^\d+$/ && $end =~ /^\d+$/) {
$seq=substr($seq,$beg,(1+$end-$beg));}}
# ------------------------------
# write output
$Lok=$msg=0;
if ($formOutLoc =~/fasta/) { ($Lok,$msg)=&fastaWrt($fileOutLoc,$id,$seq); }
elsif ($formOutLoc =~/pir/) { ($Lok,$msg)=&pirWrtOne($fileOutLoc,$id,$seq); }
elsif ($formOutLoc =~/gcg/) { ($Lok,$msg)=&gcgWrt($fileOutLoc,$id,$seq); }
return(&errSbrMsg("output format=$formOutLoc not digested!\n".$id."\n"))
if (! $Lok && ! $msg);
return(&errSbrMsg("problem writing output format=$formOutLoc, file=$fileOutLoc!\n"))
if (! $Lok);
return(1,"ok $sbrName");
} # end of convSeq2seq
#==============================================================================
sub convSeq2seqOld {
local($exeConvSeqLoc,$fileInLoc,$fileOutLoc,$formOutLoc,$frag,$fileScreenLoc,$fhTraceLoc)=@_;
local($outformat,$an,$commandLoc);
#----------------------------------------------------------------------
# convSeq2seqOld convert all sequence-only formats to sequence only
# in: $exeConvSeq,$fileIn,$fileOut,$formOutLoc,$frag,$fileScreen,$fhTraceLoc
# in: $formOutLoc= 'FASTA|GCG|PIR'
# in: $frage = 1-5, fragment from 1 -5
# out: file
# err: ok=(1,'ok'), err=(0,'msg')
#----------------------------------------------------------------------
$sbrName="lib-br:convSeq2seqOld";
$allow="fasta|pir|gcg";
return(0,"*** $sbrName: not def exeConvSeqLoc!") if (! defined $exeConvSeqLoc);
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOutLoc!") if (! defined $formOutLoc);
$fileScreenLoc=0 if (! defined $fileScreenLoc);
$frag=0 if (! defined $frag);
$fhTraceLoc="STDOUT" if (! defined $fhTraceLoc);
# check existence of files
# return(0,"*** $sbrName: no exe '$exeConvSeqLoc'!") if (! -e $exeConvSeqLoc);
return(0,"*** $sbrName: no file '$fileInLoc'!") if (! -e $fileInLoc);
# check format
$formOutLoc=~tr/[A-Z]/[a-z]/;
return(0,"*** $sbrName: output format $formOutLoc not supported\n")
if ($formOutLoc !~ /$allow/);
$anFormOut=substr($formOutLoc,1,1);$anFormOut=~tr/[a-z]/[A-Z]/;
$frag=0 if ($frag !~ /\-/);
# ------------------------------
if ($frag){ # extract fragments?
$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
$frag=0 if ($beg =~/\D/ || $end =~ /\D/);}
# ------------------------------
# call FORTRAN program
$cmd= ""; # eschew warnings
$an2= "N"; # write another format?
if ($frag){
$an1= "Y"; # do fragment
$anF= "$beg $end"; # answer for fragment
eval "\$cmd=\"$exeConvSeqLoc,$fileInLoc,$anFormOut,$an1,$anF,$fileOutLoc,$an2,\"";
($Lok,$msg)=
&sysRunProg($cmd,$fileScreenLoc,$fhTraceLoc);}
else {
$an1= "N"; # no fragment
eval "\$cmd=\"$exeConvSeqLoc,$fileInLoc,$anFormOut,$an1,$fileOutLoc,$an2,\"";
($Lok,$msg)=
&sysRunProg($cmd,$fileScreenLoc,$fhTraceLoc);}
return(&errSbrMsg("no output from FORTRAN convert_seq, could not run_program cmd=$cmd\n",
$msg)) if (! $Lok || ! -e $fileOutLoc);
return(1,"ok $sbrName");
} # end of convSeq2seqOld
#==============================================================================
sub convSwiss2fasta {
local($fileInLoc,$fileOutLoc,$fragLoc,$LshortNamesLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convSwiss2fasta converts SWISS-PROT to FASTA format
# in: $fileInLoc,$fileOutLoc,$fragLoc
# in: $fragLoc=n-m fragment to extract (optional)
# in: $LshortNamesLoc: if 1 names <=15 characters
# out: implicit: file out
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."convSwiss2fasta";$fhinLoc="FHIN_"."convSwiss2fasta";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
$fragLoc=0 if (! defined $fragLoc);
$LshortNamesLoc=0 if (! defined $LshortNamesLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# ------------------------------
($Lok,$id,$seq)= # read SWISS
&swissRdSeq($fileInLoc);
return(0,"*** ERROR $sbrName: failed to read SWISS ($fileInLoc)\n".
"*** found id=$id\n")
if (! $Lok || length($seq)<1);
undef %tmp;
$tmp{"id","1"}= $id;
$tmp{"seq","1"}=$seq;
$tmp{"NROWS"}=1;
# ------------------------------
# extract?
if ($fragLoc){($beg,$end)=split(/-/,$frag);
foreach $it (1..$tmp{"NROWS"}){
$tmp{"seq",$it}=substr($tmp{"seq",$it},$beg,($end-$beg+1));}}
$ctres=length($tmp{"seq",1});
# ------------------------------
# shorten names?
if ($LshortNamesLoc){
undef %tmp2;
foreach $it (1..$tmp{"NROWS"}){
if (length($tmp{"id",$it})<=15) {
$tmp2{$tmp{"id",$it}}=1;
next;}
# too long
$id=$tmp{"id",$it};
$id=~s/^.*\|//g; # purge paths
# purge blanks
$id=~s/\s//g if (length($id)>15);
# purge extensions
$id=~s/\.[a-z]//g if (length($id)>15);
# cleave
if (length($id)>15){
$id=substr($id,1,15);}
# not unique
if (defined $tmp2{$id}){
$id=substr($id,1,12);
$ct=1;$idtmp=$id.$ct;
while(defined $tmp2{$idtmp}){
++$ct;
last if ($ct>999);}
$id=$idtmp;}
return(0,"*** $sbrName: shoot id=$id, orig=",,", failed shortening\n")
if (defined $tmp2{$id} || length($id)>15);
$tmp2{$id}=1;
$tmp{"id",$it}=$id;
}
undef %tmp2; }
# ------------------------------
# write output
($Lok,$msg)=
&fastaWrtMul($fileOutLoc,%tmp);
return(0,"*** ERROR $sbrName: failed to write FASTAmul ($fileOutLoc)\n".
"*** msg=$msg\n") if (! $Lok);
return(2,"-*- WARN $sbrName: wrong number written\n$msg\n") if ($Lok != 1);
return(1,"ok $sbrName");
} # end of convSwiss2fasta
#==============================================================================
sub dsspGetChain {
local ($fileIn,$chainIn,$begIn,$endIn) = @_ ;
local ($Lread,$sbrName,$fhin,$aa,$aa2,$seq,$seqC,$chainRd,$pos);
$[=1;
#----------------------------------------------------------------------
# dsspGetChain extracts all chains from DSSP
# in: $file
# out: $Lok,$tmp{"chains"}='C,D,...'
# out: $tmp{"$chain","beg"},$tmp{"$chain","end"},
#----------------------------------------------------------------------
$sbrName = "lib-br:dsspGetChain" ;$fhin="fhinDssp";
open($fhin,$fileIn) || Carp::confess( "failed to open $fileIn: $!" ) ||
return(0,"*** ERROR $sbrName: failed to open input $fileIn\n");
#--------------------------------------------------
while ( <$fhin> ) { # read in file
last if ( /^ \# RESIDUE/ ); } # skip anything before data...
undef %tmp;
$chainNow=$chains="";
while ( <$fhin> ) { # read chain
$Lread=1;
$chainRd=substr($_,12,1);
$resRd= substr($_,14,1);
next if ($resRd eq "!");
$chainRd="*" if ($chainRd eq " ");
# strange
$pos= substr($_,7,5); $pos=~s/\s//g;
$posdssp= substr($_,1,5); $posdssp=~s/\s//g;
if (defined $tmp{$chainRd} &&
$chainRd ne $chainNow){
print
"--- WARN $sbrName: problem: chainRd=$chainRd, ",
"posPDB=$pos, posDSSP=$posdssp, res=$resRd, now=$chainNow, will be skipped\n";
next;}
if ($chainRd ne $chainNow){
$tmp{$chainRd}=1;
$chainNow= $chainRd;
$chains.= $chainRd.",";
$tmp{$chainRd,"begpdb"}=$pos;
$tmp{$chainRd,"beg"}= $posdssp;
}
else {
$tmp{$chainRd,"endpdb"}=$pos;
$tmp{$chainRd,"end"}= $posdssp;
}}
close($fhin);
$chains=~s/^,*|,*$//g;
# clean up strange bits
$tmp{"chains"}="";
foreach $tmp (split(/,/,$chains)){
next if (! defined $tmp{$tmp,"beg"});
next if (! defined $tmp{$tmp,"end"});
# too short
next if ( ($tmp{$tmp,"end"} - $tmp{$tmp,"beg"}) < 5);
$tmp{"chains"}.=$tmp.",";
}
$tmp{"chains"}=~s/,*$//g;
return(1,%tmp);
} # end of: dsspGetChain
#==============================================================================
sub dsspRdSeq {
local ($fileIn,$chainIn,$begIn,$endIn) = @_ ;
local ($Lread,$sbrName,$fhin,$aa,$aa2,$seq,$seqC,$chainRd,$pos);
$[=1;
#----------------------------------------------------------------------
# dsspRdSeq extracts the sequence from DSSP
# in: $file,$chain,$beg,$end
# in: for wild cards beg="", end=""
# out: $Lok,$seq,$seqC (second replaced a-z to C)
#----------------------------------------------------------------------
$sbrName = "lib-br:dsspRdSeq" ;$fhin="fhinDssp";
&open_file("$fhin","$fileIn") ||
return(0,"*** ERROR $sbrName: failed to open input $fileIn\n");
#----------------------------------------
# extract input
if (defined $chainIn && length($chainIn)>0 && $chainIn=~/[A-Z0-9]/){
$chainIn=~s/\s//g;$chainIn =~tr/[a-z]/[A-Z]/; }else{$chainIn = "*" ;}
$begIn = "*" if (! defined $begIn || length($begIn)==0); $begIn=~s/\s//g;;
$endIn = "*" if (! defined $endIn || length($endIn)==0); $endIn=~s/\s//g;;
#--------------------------------------------------
# read in file
$ctline=0;
while ( <$fhin> ) {
++$ctline;
last if ( /^ \# RESIDUE/ ); } # skip anything before data...
$seq=$seqC="";
while ( <$fhin> ) { # read sequence
++$ctline;
$Lread=1;
if (length($_)<12){
Carp::confess("*** fatal ERROR in $fileIn: line=$ctline:$_!");}
$chainRd=substr($_,12,1);
$pos= substr($_,7,5); $pos=~s/\s//g;
next if (($chainRd ne "$chainIn" && $chainIn ne "*" ) || # check chain
($begIn ne "*" && $pos < $begIn) || # check begin
($endIn ne "*" && $pos > $endIn)) ; # check end
$aa=substr($_,14,1);
$aa2=$aa;if ($aa2=~/[a-z]/){$aa2="C";} # lower case to C
$seq.=$aa;$seqC.=$aa2; } close ($fhin);
return(1,$seq,$seqC) if (length($seq)>0);
return(0);
} # end of: dsspRdSeq
#===============================================================================
sub dsspWrtFromPhd {
local ($fileOutLoc,$id_in)=@_;
local ($it,$fhoutLoc);
$[ =1 ;
#-------------------------------------------------------------------------------
# dsspWrtFromPhd
# in: $fileOutLoc
# in GLOBAL: @NUM, @SEQ, @SEC(HE ), @ACC, @RISEC, @RIACC
# in GLOBAL: $CHAIN
# out: 1|0,msg, implicit:
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."dsspWrtFromPhd"; $fhoutLoc="FHOUT_"."dsspWrtFromPhd";
# ------------------------------
# check arguments
return(&errSbr("not def fileOutLoc!")) if (! defined $fileOutLoc);
# return(&errSbr("not def !")) if (! defined $);
# return(&errSbr("miss in file '$fileInLoc'!")) if (! -e $fileInLoc);
# chain identifier
$CHAIN=" " if (! defined $CHAIN ||
length($CHAIN) != 1);
# ------------------------------
# open new file
&open_file("$fhoutLoc",">$fileOutLoc") ||
return(&errSbr("fileOutLoc=$fileOutLoc, not created"));
# ------------------------------
# DSSP header
print $fhoutLoc
"**** SECONDARY STRUCTURE DEFINITION BY THE PROGRAM DSSP, here PHD prediction\n",
"REFERENCE BURKHARD ROST (1996) METHODS IN ENZYMOLOGY, 266, 525-539\n",
"HEADER $id_in \n",
"COMPND \n",
"SOURCE \n",
"AUTHOR \n",
" \# RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA \n";
# ------------------------------
# body
# ------------------------------
for ($it=1; $it<=$#SEC; ++$it) {
# defaults
$num=$it; $riacc=0; $risec=0;
$seq="U"; $sec="U"; $acc=999;
# fill in
$num= $NUM[$it] if (defined $NUM[$it]);
$seq= $SEQ[$it] if (defined $SEQ[$it]);
$sec= $SEC[$it] if (defined $SEC[$it]);
$acc= $ACC[$it] if (defined $ACC[$it]);
$risec=$RISEC[$it] if (defined $RISEC[$it]);
$riacc=$RIACC[$it] if (defined $RIACC[$it]);
# ERROR messages
print "*** ERROR $sbrName: it=$it, SEQ not defined\n" if ($seq eq "U" );
print "*** ERROR $sbrName: it=$it, SEC not defined\n" if ($sec eq "U" );
print "*** ERROR $sbrName: it=$it, ACC not defined\n" if ($acc eq "999");
# write it
printf $fhoutLoc
" %4d %4d %1s %1s %1s 0 0 %3d %1d %1d\n",
$num, $num, $CHAIN, $seq, $sec, $acc, $risec, $riacc;
}
close($fhoutLoc);
return(1,"ok");
} # end of dsspWrtFromPhd
#==============================================================================
sub errSbr {local($txtInLoc,$sbrNameLocy) = @_ ;
#-------------------------------------------------------------------------------
# errSbr simply writes '*** ERROR $sbrName: $txtInLoc'
#-------------------------------------------------------------------------------
$sbrNameLocy=$sbrName if (! defined $sbrNameLocy);
$txtInLoc.="\n";
$txtInLoc=~s/\n\n+/\n/g;
return(0,"*** ERROR $sbrNameLocy: $txtInLoc");
} # end of errSbr
#==============================================================================
sub errSbrMsg {local($txtInLoc,$msgInLoc,$sbrNameLocy) = @_ ;
#-------------------------------------------------------------------------------
# errSbrMsg simply writes '*** ERROR $sbrName: $txtInLoc\n'.$msg
#-------------------------------------------------------------------------------
$sbrNameLocy=$sbrName if (! defined $sbrNameLocy);
$txtInLoc.="\n";
$txtInLoc=~s/\n\n+/\n/g;
$msgInLoc.="\n";
$msgInLoc=~s/\n\n+/\n/g;
return(0,"*** ERROR $sbrNameLocy: $txtInLoc".$msgInLoc);
} # end of errSbrMsg
#==============================================================================
sub fastaRdGuide {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# fastaRdGuide reads first sequence in list of FASTA format
# in: $fileInLoc,$fhErrSbr
# out: 0|1,$id,$seq
# err: ok=(1,id,seq), err=(0,'msg',)
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName="$tmp"."fastaRdGuide";$fhinLoc="FHIN"."$sbrName";
$Lok= &open_file("$fhinLoc","$fileInLoc");
return(0,"*** ERROR $sbrName: old '$fileInLoc' not opened\n"," ") if (! $Lok);
$ct=0;$seq="";
while (<$fhinLoc>) {
$_=~s/\n//g;
if ($_=~/^\s*>\s*(.+)$/){
++$ct;
last if ($ct>1);
$id=$1;$id=~s/[\s\t]+/ /g;
# $id=~s/^[^A-Za-z0-9]*|[^A-Za-z0-9]*$//g;
next;}
$seq.="$_";}
$seq=~s/\s//g;
return(0,"*** ERROR $sbrName: no guide sequence found\n"," ") if (length($seq)<1);
return(1,$id,$seq);
} # end of fastaRdGuide
#===============================================================================
sub fastaRdMul {
local($fileInLoc,$rd) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# fastaRdMul reads many sequences in FASTA db
# in: $fileInLoc,$rd with:
# $rd = '1,5,6', i.e. list of numbers to read
# $rd = 'id1,id2', i.e. list of ids to read
# NOTE: numbers faster!!!
# out: 1|0,$id,$seq (note: many ids/seq separated by '\n'
# err: ok=(1,id,seq), err=(0,'msg')
#-------------------------------------------------------------------------------
$sbrName="lib-br:fastaRdMul";$fhinLoc="FHIN_"."$sbrName";
&open_file("$fhinLoc","$fileInLoc") ||
return(0,"*** ERROR $sbrName: old '$fileInLoc' not opened\n"," ");
undef %tmp;
if (! defined $rd) {
$LisNumber=1;
$rd=0;}
elsif ($rd !~ /[^0-9\,]/){
@tmp=split(/,/,$rd);
$LisNumber=1;
foreach $tmp(@tmp){$tmp{$tmp}=1;}}
else {$LisNumber=0;
@tmp=split(/,/,$rd); }
$ct=$ctRd=0;
while (<$fhinLoc>) {
$_=~s/\n//g;
if ($_=~/^\s*>\s*(.+)$/){ # line with id
++$ct;$Lread=0;
last if ($rd && $ctRd==$#tmp); # fin if all found
next if ($rd && $LisNumber && ! defined $tmp{$ct});
$id=$1;$id=~s/\s\s*/ /g;$id=~s/^[^A-Za-z0-9]*|[^A-Za-z0-9]*$//g;
$Lread=1 if ( ($LisNumber && defined $tmp{$ct})
|| $rd == 0);
if (! $Lread){ # go through all ids
foreach $tmp(@tmp){
next if ($tmp !~/$id/);
$Lread=1; # does match, so take
last;}}
next if (! $Lread);
++$ctRd;
$tmp{"$ctRd","id"}=$id;
$tmp{"$ctRd","seq"}="";}
elsif ($Lread) { # line with sequence
$tmp{"$ctRd","seq"}.="$_";}}
$seq=$id=""; # join to long strings
foreach $it (1..$ctRd) { $id.= $tmp{"$it","id"}."\n";
$tmp{"$it","seq"}=~s/\s//g;
$seq.=$tmp{"$it","seq"}."\n";}
$#tmp=0; # save memory
undef %tmp; # save memory
return(0,"*** ERROR $sbrName: file=$fileInLoc, nali=$ct, wanted: (rd=$rd)\n"," ")
if (length($seq)<1);
return(1,$id,$seq);
} # end of fastaRdMul
#===============================================================================
sub fastaWrt {
local($fileOutLoc,$id,$seqLoc) = @_ ;
local($sbrName,$fhoutLoc,$tmp,$Lok,$idloc);
$[ =1 ;
#-------------------------------------------------------------------------------
# fastaWrt writes a sequence in FASTA format
# in: $fileOut,$id,$seq (one string)
# out:
# err: ok=(1,'ok'), err=(0,'msg')
#-------------------------------------------------------------------------------
$sbrName="lib-br:fastaWrt";$fhoutLoc="FHOUT_"."$sbrName";
# print "yy into write seq=$seqLoc,\n";
&open_file("$fhoutLoc",">$fileOutLoc") ||
return(0,"*** ERROR $sbrName: '$fileOutLoc' not opened for write\n");
# 2003-09: br remove stuff
$idloc=$id;
$idloc=~s/\n//g;
$idloc=~s/^\s*|\s*$//g;
print $fhoutLoc ">".$idloc."\n";
for($it=1;$it<=length($seqLoc);$it+=50){
$tmpwrt="";
foreach $it2 (0..4){
last if (($it+10*$it2)>=length($seqLoc));
$tmp=substr($seqLoc,($it+10*$it2),10);
$tmp=~s/^\s*|\s*$//g;
next if ($tmp=~/^\s*$/);
$tmpwrt.=sprintf(" %-10s",$tmp);
}
$tmpwrt=~s/^\s*|\s*$//g;
$tmpwrt.="\n";
print $fhoutLoc $tmpwrt;
}
close($fhoutLoc);
return(1,"ok $sbrName");
} # end of fastaWrt
#==============================================================================
sub fastaWrtMul {
local($fileOutLoc,%tmp) = @_ ;
local($sbrName,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# fastaWrtMul writes a list of sequences in FASTA format
# in: $fileOut,$tmp{} with:
# in: $tmp{"NROWS"} number of sequences
# in: $tmp{"id",$ct} id for sequence $ct
# in: $tmp{"seq",$ct} seq for sequence $ct
# out: file
# err: err -> 0,message
# err: ok -> 1,ok
# err: warn -> 2,not enough written
#-------------------------------------------------------------------------------
$sbrName="lib-br:fastaWrtMul";$fhoutLoc="FHOUT_"."$sbrName";
return(0,"*** ERROR $sbrName: no tmp{NROWS} defined\n") if (! defined $tmp{"NROWS"});
&open_file("$fhoutLoc",">$fileOutLoc") ||
return(0,"*** ERROR $sbrName: '$fileOutLoc' not opened for write\n");
$ctOk=0;
foreach $itpair (1..$tmp{"NROWS"}){
next if (! defined $tmp{"id",$itpair} || ! defined $tmp{"seq",$itpair});
++$ctOk;
# some massage
$tmp{"id",$itpair}=~s/[\s\t\n]+/ /g;
$tmp{"seq",$itpair}=~s/[\s\t\n]+//g;
# write
print $fhoutLoc ">",$tmp{"id",$itpair},"\n";
$lenHere=length($tmp{"seq",$itpair});
for($it=1; $it<=$lenHere; $it+=50){
$tmpWrt= "";
foreach $it2 (0..4){
$itHere=($it + 10*$it2);
last if ( $itHere >= $lenHere);
$nchunk=10;
$nchunk=1+($lenHere-$itHere) if ( (10 + $itHere) > $lenHere);
$tmpWrt.= sprintf(" %-10s",substr($tmp{"seq",$itpair},$itHere,$nchunk));
}
print $fhoutLoc $tmpWrt,"\n";
}
}
close($fhoutLoc);
return(0,"*** ERROR $sbrName: no sequence written\n")
if (! $ctOk);
return(2,"-*- WARN $sbrName: wrote fewer sequences than expected\n")
if ($ctOk!=$tmp{"NROWS"});
return(1,"ok $sbrName");
} # end of fastaWrtMul
#==============================================================================
sub fctRunTimeLeft {
local($timeBegLoc,$num_to_run,$num_did_run) = @_ ;
local($sbrName);
$[ =1 ;
#-------------------------------------------------------------------------------
# fctRunTimeLeft estimates the time the job still needs to run
# in: $timeBegLoc : time (time) when job began
# in: $num_to_run : number of things to do
# in: $num_did_run: number of things that are done, so far
# out: $_string_time-still (hour:min:sec)
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."fctRunTimeLeft";
$timeNow=time;
$timeRun=$timeNow-$timeBegLoc;
$percLoc=0;
$percLoc=100*($num_did_run/$num_to_run) if ($num_to_run > 0);
if ($percLoc) {
$timeTot=int(100*($timeRun/$percLoc));
$timeLeft=$timeTot-$timeRun;
$tmp=
&fctSeconds2time($timeLeft);
@tmp=split(/:/,$tmp); foreach $tmp (@tmp){$tmp=~s/^0//g;}
$estimateLoc= "";
$estimateLoc.= $tmp[1]."h " if ($tmp[1] > 9);
$estimateLoc.=" ".$tmp[1]."h " if (9 >= $tmp[1] && $tmp[1] > 0);
$estimateLoc.= $tmp[2]."m " if ($tmp[2] > 9);
$estimateLoc.=" ".$tmp[2]."m " if (9 >= $tmp[2] && $tmp[2] > 0);
$estimateLoc.=" "." ". " " if ($tmp[2] <= 0 && $tmp[1] > 0);
$estimateLoc.= $tmp[3]."s " if ($tmp[3] > 9);
$estimateLoc.=" ".$tmp[3]."s " if (9 >= $tmp[3] && $tmp[3] > 0);
$estimateLoc.=" "." ". " " if ($tmp[3] <= 0 && ($tmp[1] > 0 || $tmp[2] > 0));
$estimateLoc= "done" if (length($estimateLoc) < 1);}
else {
$estimateLoc="?";}
return($estimateLoc);
} # end of fctRunTimeLeft
#==============================================================================
sub fctSeconds2time {
local($secIn) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# fctSeconds2time converts seconds to hours:minutes:seconds
# in: seconds
# out: 05:13:50
#-------------------------------------------------------------------------------
$sbrName="lib-comp:"."fctSeconds2time";$fhinLoc="FHIN"."$sbrName";
$minTmp= int($secIn/60);
$seconds= ($secIn - $minTmp*60); $seconds=int($seconds);
$hours= int($minTmp/60); $hours= int($hours);
$minutes= ($minTmp - $hours*60); $minutes=int($minutes);
$seconds="0".$seconds if (length($seconds)==1);
$minutes="0".$minutes if (length($minutes)==1);
$hours= "0".$hours if (length($hours)==1);
return("$hours".":".$minutes.":".$seconds);
} # end of fctSeconds2time
#==============================================================================
sub gcgRd {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# gcgRd reads sequence in GCG format
# in: $fileInLoc
# out: 1|0,$id,$seq
# err: ok=(1,id,seq), err=(0,'msg')
#-------------------------------------------------------------------------------
$sbrName="lib-br:gcgRd";$fhinLoc="FHIN_"."$sbrName";
&open_file("$fhinLoc","$fileInLoc") ||
return(0,"*** ERROR $sbrName: old '$fileInLoc' not opened\n"," ");
$seq="";
while (<$fhinLoc>) {
$_=~s/\n//g;$line=$_;
if ($line=~/^\s*(\S+)\s*from\s*:/){
$id=$1;
next;}
next if ($line !~ /^\s*\d+\s+(.*)$/);
$tmp=$1;$tmp=~s/\s//g;
$seq.=$tmp;}close($fhinLoc);
return(0,"*** ERROR $sbrName: file=$fileInLoc, no sequence found\n") if (length($seq)<1);
return(1,$id,$seq);
} # end of gcgRd
#===============================================================================
sub gcgWrt {
local($fileOutLoc,$idLoc,$seqLoc) = @_ ;
local($sbrName,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# gcgWrt writes one sequence in GCG format
# in: $fileOut,$id,$seq,
# out: file
# err: err -> 0,message
# err: ok -> 1,ok
#-------------------------------------------------------------------------------
$sbrName="lib-br:gcgWrt";$fhoutLoc="FHOUT_"."$sbrName";
return(0,"*** ERROR $sbrName: no seq defined\n") if (! defined $seqLoc);
&open_file("$fhoutLoc",">$fileOutLoc") ||
return(0,"*** ERROR $sbrName: '$fileOutLoc' not opened for write\n");
#....,....1....,....2....,....3....,....4....,....5....,....6....,....7
#1ppt.f from: 1 to: 36
#
#1ppt
# 1ppt.gcg Length: 36 24-Feb-99 Check: 2818 ..
#
# 1 GPSQPTYPGD DAPVEDLIRF YDNLQQYLNV VTRHRY
# some massage
$idLoc=~s/[\s\t\n]+/ /g;
$seqLoc=~s/[\s\t\n]+//g;
# write
printf $fhoutLoc "%-s from: %5d to:%5d\n",$idLoc,1,length($seqLoc);
print $fhoutLoc "\n";
print $fhoutLoc $idLoc,"\n";
printf $fhoutLoc
" %-s Length:%5d 11-Jul-99 Check: 2818 ..\n",$fileOutLoc,length($seqLoc);
print $fhoutLoc "\n";
# ------------------------------
# sequence
$len=length($seqLoc);
$num=1+int($len/50);
$lenSub=10;
foreach $it (1..$num) {
$beg=($it-1)*50+1;
$end=$it*50;
last if ($beg > $len);
printf $fhoutLoc "%8d ",$beg;
foreach $it2 (1..5) {
$beg2=$beg+($it2-1)*10;
last if ($beg2 > $len);
$tmp=1+$len-$beg2;
$lenSub=$tmp if ($tmp < 10);
print $fhoutLoc " ",substr($seqLoc,$beg2,$lenSub);
last if ($lenSub < 10); }
print $fhoutLoc "\n\n"; }
close($fhoutLoc);
return(0,"*** ERROR $sbrName: no sequence written\n")
if (! -e $fileOutLoc);
return(1,"ok $sbrName");
} # end of gcgWrt
#==============================================================================
sub get_in_keyboard {
local($des,$def,$pre,$Lmirror)=@_;local($txt);
#--------------------------------------------------------------------------------
# get_in_keyboard gets info from keyboard
# in: $des : keyword to get
# in: $def : default settings
# in: $pre : text string beginning screen output
# default '--- '
# in: $Lmirror: if true, the default is mirrored
# out: $val : value obtained
#--------------------------------------------------------------------------------
$pre= "---" if (! defined $pre);
$Lmirror=0 if (! defined $Lmirror || ! $Lmirror);
$txt=""; # ini
printf "%-s %-s\n", $pre,"-" x (79 - length($pre));
printf "%-s %-15s:%-s\n", $pre,"type value for",$des;
if (defined $def){
printf "%-s %-15s:%-s\n",$pre,"type RETURN to enter value, or to keep default";
printf "%-s %-15s>%-s\n",$pre,"default value",$def;}
else {
printf "%-s %-15s>%-s\n",$pre,"type RETURN to enter value"; }
$txt=$def if ($Lmirror); # mirror it
printf "%-s %-15s>%-s", $pre,"type",$txt;
while(<STDIN>){
$txt.=$_;
last if ($_=~/\n/);} $txt=~s/^\s+|\s+$//g;
$txt=$def if (length($txt) < 1);
printf "%-s %-15s>%-s\n", $pre,"--> you chose",$txt;
return ($txt);
} # end of get_in_keyboard
#==============================================================================
sub get_range {
local ($range_txt,$nall) = @_;
local (@range,@rangeLoc,$it,$range1,$range2);
$[ =1 ;
#--------------------------------------------------------------------------------
# get_range converts range=n1-n2 into @range (1,2)
# in: 'n1-n2' NALL: e.g. incl=1-5,9,15
# n1= begin, n2 = end, * for wild card
# NALL = number of last position
# out: @takeLoc: begin,begin+1,...,end-1,end
#--------------------------------------------------------------------------------
$#range=0;
if (! defined $range_txt || length($range_txt)<1 || $range_txt eq "unk"
|| $range_txt !~/\d/ ) {
print
"*** ERROR in get_range: argument: range=$range_txt, nall=$nall, not digestable\n";
return(0);}
$range_txt=~s/\s//g; # purge blanks
$nall=0 if (! defined $nall);
# already only a number
return($range_txt) if ($range_txt !~/[^0-9]/);
if ($range_txt !~/[\-,]/) { # no range given
print "*** ERROR in get_range: argument: '$range_txt,$nall' not digestable\n";
return(0);}
# ------------------------------
# dissect commata
if ($range_txt =~ /\,/) {
@range=split(/,/,$range_txt);}
# ------------------------------
# dissect hyphens
elsif ($range_txt =~ /(\d*|\*)-(\d*|\*)/) {
@range=&get_rangeHyphen($range_txt,$nall);}
# ------------------------------
# process further elements with hyphens
$#range2=0;
foreach $range (@range){
if ($range =~ /(\d*|\*)-(\d*|\*)/) {
push(@range2,&get_rangeHyphen($range,$nall));}
else {
push(@range2,$range);}}
@range=@range2; $#range2=0;
# ------------------------------
if ($#range>1){ # sort
@range=sort {$a<=>$b} @range;}
return (@range);
} # end of get_range
#==============================================================================
sub get_rangeHyphen {
local ($range_txt,$nall) = @_ ;
local (@rangeLoc,$it,$range1,$range2);
$[ =1 ;
#--------------------------------------------------------------------------------
# get_rangeHyphen reads 'n1-n2'
# in: 'n1-n2', NALL (n1= begin, n2 = end, * for wild card)
# NALL = number of last position
# out: begin,begin+1,...,end-1,end
#--------------------------------------------------------------------------------
if ($range_txt =~ /(\d*|\*)-(\d*|\*)/) {
($range1,$range2)=split(/-/,$range_txt);
if ($range1=~/\*/) {$range1=1;}
if ($range2=~/\*/) {$range2=$nall;}
for($it=$range1;$it<=$range2;++$it) {push(@rangeLoc,$it);} }
else { @rangeLoc=($range_txt);}
return(@rangeLoc);
} # end of get_rangeHyphen
#===============================================================================
sub getDistanceNewCurveIde {
local($laliLoc)=@_; local($expon,$loc);
$[ =1 ;
#-------------------------------------------------------------------------------
# getDistanceNewCurveIde out= pide value for new curve
# br 2003-08: mistake corrected
#
# in: $lali
# out: $pide
#
# OLD pide= 510 * L ^ { -0.32 (1 + e ^-(L/1000)) }
# NEW pide= 480 * L ^ { -0.32 (1 + e ^-(L/1000)) }
#-------------------------------------------------------------------------------
$sbrName="lib-br:getDistanceNewCurveIde";
return(0,"*** ERROR $sbrName: lali not defined \n") if (! defined $laliLoc);
return(0,"*** ERROR $sbrName: '$laliLoc' = alignment length??\n")
if (length($laliLoc)<1 || $laliLoc=~/[^0-9.]/);
# saturation short: <=11
return(100,"ok $sbrName saturation short")
if ($laliLoc<=11);
# saturation long: >450
return(19.5,"ok $sbrName saturation long")
if ($laliLoc>450);
$expon= - 0.32 * ( 1 + exp (-$laliLoc/1000) );
# $loc= 510 * $laliLoc ** ($expon);
$loc= 480 * $laliLoc ** ($expon);
$loc=100 if ($loc > 100); # saturation short
$loc=19.5 if ($loc < 19.5); # saturation long
return($loc,"ok $sbrName");
} # end of getDistanceNewCurveIde
#==============================================================================
sub getFileFormatQuick {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# getFileFormatQuick quick scan for file format: assumptions
# file exists
# file is db format (i.e. no list)
# in: file
# out: 0|1,format
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."getFileFormatQuick";$fhinLoc="FHIN_"."getFileFormatQuick";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# alignments (EMBL 1)
return(1,"HSSP") if (&is_hssp($fileInLoc));
return(1,"STRIP") if (&is_strip($fileInLoc));
# return(1,"STRIPOLD") if (&is_strip_old($fileInLoc));
return(1,"DSSP") if (&is_dssp($fileInLoc));
return(1,"FSSP") if (&is_fssp($fileInLoc));
# alignments (EMBL 1)
return(1,"DAF") if (&isDaf($fileInLoc));
return(1,"SAF") if (&isSaf($fileInLoc));
# alignments other
return(1,"MSF") if (&isMsf($fileInLoc));
return(1,"FASTAMUL") if (&isFastaMul($fileInLoc));
return(1,"PIRMUL") if (&isPirMul($fileInLoc));
# sequences
return(1,"FASTA") if (&isFasta($fileInLoc));
return(1,"SWISS") if (&isSwiss($fileInLoc));
return(1,"PIR") if (&isPir($fileInLoc));
return(1,"GCG") if (&isGcg($fileInLoc));
return(1,"PDB") if (&isPdb($fileInLoc));
# PP
return(1,"PPCOL") if (&is_ppcol($fileInLoc));
# NN
return(1,"NNDB") if (&is_rdb_nnDb($fileInLoc));
# PHD
return(1,"PHDRDBBOTH") if (&isPhdBoth($fileInLoc));
return(1,"PHDRDBACC") if (&isPhdAcc($fileInLoc));
return(1,"PHDRDBHTM") if (&isPhdHtm($fileInLoc));
return(1,"PHDRDBHTMREF") if (&is_rdb_htmref($fileInLoc));
return(1,"PHDRDBHTMTOP") if (&is_rdb_htmtop($fileInLoc));
return(1,"PHDRDBSEC") if (&isPhdSec($fileInLoc));
# RDB
return(1,"RDB") if (&isRdb($fileInLoc));
return(1,"unk");
} # end of getFileFormatQuick
#===============================================================================
sub getSysARCH {
# DEPRECATED DEPRECATED DEPRECATED DEPRECATED DEPRECATED
# 01/10/10 GY
# WE ARE NO LONGER LOOKING FOR PLATFORM INFORMATION USING THIS METHOD
# local($exePvmgetarch,@argLoc) = @_ ;
# local($sbrName,$Lok);
# $[ =1 ;
#-------------------------------------------------------------------------------
# getSysARCH tries to get the system architecture
#
# in: $exePvmgetarch: bin-shell script to get ARCH
# = 0 to not execute that one..
# in: @argLoc: all arguments passed to program, checks
# for one with:
# ARCH=SGI64 .. or so
# out: <0,$ARCH>
#-------------------------------------------------------------------------------
# $tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";$sbrName=$tmp."getSysARCH";
# $archFound=0;
# $exePvmgetarch=0 if (! defined $exePvmgetarch);
# ------------------------------
# (1) find in arguments passed
# ------------------------------
# if (defined @argLoc && $#argLoc > 0) {
# foreach $arg (@argLoc) {
# if ($arg=~/^ARCH=(\S+)/i) {
# $archFound=$1;
# archs are upper case: convert
# $archFound=~tr/[a-z]/[A-Z]/;
# last; }} }
# return($archFound) if ($archFound);
# ------------------------------
# (2) try env asf
# ------------------------------
# $archFound=$ENV{'ARCH'} || $ENV{'CPUARC'} || 0;
# return($archFound) if ($archFound);
# ------------------------------
# (3) run bin shell script given
# ------------------------------
# if ($exePvmgetarch && (-e $exePvmgetarch || -l $exePvmgetarch)) {
# $scr=$exePvmgetarch;
# $archFound=`$scr`; # system call
# $archFound=~s/\s|\n//g;
# $archFound=0 if (length($archFound < 3) || $archFound !~ /[A-Z][A-Z]/);}
# return($archFound) if ($archFound);
# ------------------------------
# (4) search bin shell script
# ------------------------------
# foreach $possible ("/home/rost/pub/phd/scr/pvmgetarch.sh",
# "/home/rost/etc/pvmgetarch.sh") {
# if (-e $possible || -l $possible) {
# $exePvmgetarch=$possible;
# last; }}
# somewhere in relative paths
# if (! $exePvmgetarch) {
# $dirRelative=$0; $dirRelative=~s/\.\///g; $dirRelative=~s/^(.*\/).*$/$1/;
# foreach $possible ("scr/pvmgetarch.sh","scr/which_arch.sh",
# "bin/pvmgetarch.sh","bin/which_arch.sh",
# "etc/pvmgetarch.sh","etc/which_arch.sh",
# "pvmgetarch.sh","which_arch.sh") {
# if (-e $possible || -l $possible) {
# $exePvmgetarch=$possible;
# last; }}}
# ******************************
# script not found
# return(0) if (! $exePvmgetarch);
# ******************************
# ------------------------------
# (5) run bin shell script
# ------------------------------
# $scr=$exePvmgetarch;
# $archFound=`$scr`; # system call
# $archFound=~s/\s|\n//g;
# $archFound=0 if (length($archFound) < 3 || $archFound !~ /[A-Z][A-Z]/);
# return($archFound);
} # end of getSysARCH
#===============================================================================
sub hsspCorrectNali {
local($fileInLoc,$fileTmpLoc,$fhErrSbr) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# hsspCorrectNali convert_seq makes mistakes in NALI
# these are corrected here!
# in: $fileInLoc
# in: $fileInLoc
# out: 1|0,msg, implicit:
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."hsspCorrectNali";
$fhinLoc="FHIN_"."hsspCorrectNali";$fhoutLoc="FHOUT_"."hsspCorrectNali";
# check arguments
return(&errSbr("not def fileInLoc!")) if (! defined $fileInLoc);
return(&errSbr("not def fileTmpLoc!")) if (! defined $fileTmpLoc);
# return(&errSbr("not def !")) if (! defined $);
return(&errSbr("no fileIn=$fileInLoc!")) if (! -e $fileInLoc);
# open file
open($fhinLoc,$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(&errSbr("fileInLoc=$fileInLoc, not opened"));
# ------------------------------
while (<$fhinLoc>) { # read file
if ($_=~/^NALIGN \s+(\d+)/){
$nalign=$1;
}
elsif ($_=~/^\s+(\d+)\s\:\s/){
$itali=$1;
}
elsif ($_=~/^\#\# ALIGNMENTS/){
last;
}
}
close($fhinLoc);
# ------------------------------
# ok?
if ($itali==$nalign){
return(1,"ok $sbrName no change");
}
# change:
print $fhErrSbr
"--- file.hssp ($fileInLoc) NALI=$nalign, itali=$itali-> have to change it!\n"
if ($par{"debug"});
# move files
$cmd="\\mv ".$fileInLoc." ".$fileTmpLoc;
($Lok,$msg)=&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
return(0,"*** ERROR $sbrName: failed to run system ($cmd)\n".$msg."\n")
if (! $Lok || ! -e $fileTmpLoc);
print $fhErrSbr
"--- $sbrName system '$cmd'\n"
if ($par{"debug"});
# now change
open($fhinLoc,$fileTmpLoc) || Carp::confess( "failed to open $fileTmpLoc: $!" ) || return(&errSbr("in fileTmpLoc=$fileTmpLoc, not opened"));
open($fhoutLoc,">".$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(&errSbr("out fileInLoc=$fileInLoc, not created"));
# ------------------------------
while (<$fhinLoc>) { # read file
if ($_=~/^NALIGN \s+(\d+)/){
# '....,....1....,'
# 'NALIGN 64'
printf $fhoutLoc
"NALIGN %8d\n",$itali;
}
else {
print $fhoutLoc $_;
}
}
close($fhinLoc);
close($fhoutLoc);
return(1,"ok $sbrName");
} # end of hsspCorrectNali
#==============================================================================
sub hsspGetChain {
local ($fileIn) = @_ ;
local ($fhin,$ifirLoc,$ilasLoc,$tmp1,$tmp2,
$chainLoc,$posLoc,$posRd,$chainRd,@cLoc,@pLoc,%rdLoc);
$[ =1 ;
#--------------------------------------------------------------------------------
# hsspGetChain extracts all chain identifiers in HSSP file
# in: $file
# out: $chains (ABC) ,%rdLoc
# no chain -> $chains=' '
# out $rdLoc{"NROWS"},$rdLoc{"$ct","chain"},
# out $rdLoc{"$ct","ifir"},$rdLoc{"$ct","ilas"}
#--------------------------------------------------------------------------------
$fhin="FhInHssp";
return(0,"no file") if (! -e $fileIn);
&open_file("$fhin","$fileIn");
while(<$fhin>){ # until start of data
last if ($_=~/^ SeqNo/);}
$chainLoc=$posLoc="";
while(<$fhin>){
if ($_=~/^\#/ && (length($chainLoc)>1) ) {
$posLoc.="$ifirLoc-$ilasLoc".",";
last;}
$chainRd=substr($_,13,1);
$aaRd= substr($_,15,1);
$posRd= substr($_,1,6);$posRd=~s/\s//g;
next if ($aaRd eq "!") ; # skip over chain break
if ($chainLoc !~/$chainRd/){ # new chain?
$posLoc.= "$ifirLoc-$ilasLoc"."," if (length($chainLoc)>1);
$chainLoc.= "$chainRd".",";
$ifirLoc=$ilasLoc=$posRd;}
else {
$ilasLoc=$posRd;}
}close($fhin);
$chainLoc=~s/^,|,$//g;
$posLoc=~s/\s//g;$posLoc=~s/^,|,$//g; # purge leading ','
# now split chains read
undef %rdLoc; $ctLoc=0;
@cLoc=split(/,/,$chainLoc);
@pLoc=split(/,/,$posLoc);
foreach $itLoc(1..$#cLoc){
($tmp1,$tmp2)=split(/-/,$pLoc[$itLoc]);
next if ($tmp2 == $tmp1); # exclude chains of length 1
++$ctLoc;
$rdLoc{"NROWS"}= $ctLoc;
$rdLoc{"$ctLoc","chain"}=$cLoc[$itLoc];
$rdLoc{"$ctLoc","ifir"}= $tmp1;
$rdLoc{"$ctLoc","ilas"}= $tmp2;}
$chainLoc=~s/,//g;
return($chainLoc,%rdLoc);
} # end of hsspGetChain
#==============================================================================
sub hsspGetChainLength {
local ($fileIn,$chainLoc) = @_ ;
local ($file_hssp,$ct,$tmp,$beg,$end,$pos);
$[ =1 ;
#--------------------------------------------------------------------------------
# hsspGetChainLength extracts the length of a chain in an HSSP file
# in: hssp_file,chain,
# out: $length,$ifir,$ilas
#--------------------------------------------------------------------------------
$fileIn=~s/\s//g;$fileIn=~s/\n//g;
$file_hssp=$fileIn; $Lchain=1;
$Lchain=0 if ($chainLoc eq "*" || ! &is_chain($chainLoc));
if (! -e $file_hssp){
print "*** ERROR hsspGetChainLength: no HSSP=$fileIn,\n";
return(0,"*** ERROR hsspGetChainLength: no HSSP=$fileIn,");}
&open_file("FHIN", "$file_hssp") ||
return(0,"*** ERROR hsspGetChainLength: failed opening HSSP=$fileIn,");
while ( <FHIN> ) {
last if (/^ SeqNo/); }
$ct=$pos=0;
while ( <FHIN> ) {
last if (/^\#\# /);
++$pos;$tmp=substr($_,13,1);
if ( $Lchain && ($tmp eq $chainLoc) ) { ++$ct; }
elsif ( ! $Lchain ) { ++$ct; }
elsif ( $ct>1 ) {
last;}
$beg=$pos if ($ct==1); } close(FHIN);
$end=$pos;
return($ct,$beg,$end);
} # end of hsspGetChainLength
#==============================================================================
sub hsspRdAli {
local ($fileInLoc,@want) = @_ ;
local ($sbrName,$fhinLoc,$tmp);
$[ =1 ;
#-------------------------------------------------------------------------------
# hsspRdAli reads and writes the sequence of HSSP + 70 alis
# in: $fileHssp (must exist),
# @des (1) =1, 2, ..., i.e. number of sequence to be read
# (2) = swiss_id1, swiss_id2, i.e. identifiers to read
# (3) = all (or undefined)
# NOTE: you can give ids AND numbers ('1','paho_chick','2') ..
# furthermore:
# if @want = 'seq|seqAli|seqNoins'
# only those will be returned (e.g. $tmp{"seq",$ct})
# default: all 3!
# out: 1|0,$rd{} with:
# err: (0,$msg)
# overall:
# $rd{"NROWS"}= : number of alis, i.e. $#want
# $rd{"NRES"}=N : number of residues in guide
# $rd{"SWISS"}='sw1,sw2' : list of swiss-ids read
# $rd{"0"}='pdbid' : id of guide sequence (in file header)
# $rd{$it}='sw$ct' : swiss id of the it-th alignment
# $rd{"$id"}='$it' : position of $id in final list
# $rd{"sec","$itres"} : secondary structure for residue itres
# $rd{"acc","$itres"} : accessibility for residue itres
# $rd{"chn","$itres"} : chain for residue itres
# per prot:
# $rd{"seqNoins",$ct}=sequences without insertions
# $rd{"seqNoins","0"}= GUIDE sequence
# $rd{"seq",$ct}=SEQW : sequences, with all insertions
# but NOT aligned!!!
# $rd{"seqAli",$ct} : sequences, with all insertions,
# AND aligned (all, including guide
# filled up with '.' !!
#-------------------------------------------------------------------------------
$sbrName="lib-br:hsspRdAli"; $fhinLoc="FHIN"."$sbrName"; $fhinLoc=~tr/[a-z]/[A-Z]/;
# file existing?
if ((! -e $fileInLoc) || (! &is_hssp($fileInLoc))){
print "*** ERROR $sbrName no HSSP file '$fileInLoc'\n";
return(0);}
# ------------------------------
# HSSP file format settings
$regexpBegAli= "^\#\# ALIGNMENTS"; # begin of reading
$regexpEndAli= "^\#\# SEQUENCE PROFILE"; # end of reading
$regexpSkip= "^ SeqNo"; # skip lines with pattern
$nmaxBlocks= 100; # maximal number of blocks considered (=7000 alis!)
$regexpBegIns= "^\#\# INSERTION LIST"; # begin of reading insertion list
undef %tmp; undef @seqNo; undef %seqNo;
# ------------------------------
# pointers
undef %ptr_id2num; # $ptr{xyz}= N : id=xyz is the Nth ali
undef @ptr_num2id; # $ptr[N]= xyz : Nth ali has id= xyz
undef @ptr_numWant2numFin; # $ptr[N]= M : the Nth ali is the Mth one in the list
# of all numbers wanted (i.e. = $want[M])
undef @ptr_numFin2numWant; # $ptr[M]= N : see previous, the other way around!
$#want=0 if (! defined @want);
$LreadAll=0;
# ------------------------------
# digest input
$#tmp=0; undef %kwd; # (1) detect keywords
foreach $tmp (@want){
if ($tmp=~/^(seq|seqAli|seqNoins)$/){
$kwd{$tmp}=1;
next;}
push(@tmp,$tmp);}
if (($#want>0) && ($#want == $#tmp) ){ # default keyworkds
foreach $des ("seq","seqAli","seqNoins"){
$kwd{"$des"}=1;}}
@want=@tmp;
# (2) all?
$LreadAll=1 if ( ! @want || ! $want[1] || ($want[1] eq "all"));
if (! $LreadAll){ # (3) read some
$#wantNum=$#wantId=0;
foreach $want (@want) {
if ($want !~ /[^0-9]/){push(@wantNum,$want);} # is number
else {push(@wantId,$want);}}} # is id
# ------------------------------
# get numbers/ids to read
($Lok,%rdHeader)=
&hsspRdHeader($fileInLoc,"SEQLENGTH","PDBID","NR","ID");
if (! $Lok){
print "*** ERROR $sbrName reading header of HSSP file '$fileInLoc'\n";
return(0);}
$tmp{"NRES"}= $rdHeader{"SEQLENGTH"};$tmp{"NRES"}=~s/\s//g;
$tmp{"0"}= $rdHeader{"PDBID"}; $tmp{"0"}=~s/\s//g;
$idGuide= $tmp{"0"};
$#locNum=$#locId=0; # store the translation name/number
foreach $it (1..$rdHeader{"NROWS"}){
$num=$rdHeader{"NR",$it}; $id=$rdHeader{"ID",$it};
push(@locNum,$num);push(@locId,$id);
$ptr_id2num{"$id"}=$num;
$ptr_num2id[$num]=$id;}
push(@locNum,"1") if ($#locNum==0); # nali=1
# ------------------------------
foreach $want (@wantId){ # CASE: input=list of names
$Lok=0; # -> add to @wantNum
foreach $loc (@locId){
if ($want eq $loc){$Lok=1;push(@wantNum,$ptr_id2num{"$loc"});
last;}}
if (! $Lok){
print "-*- WARNING $sbrName wanted id '$want' not in '$fileInLoc'\n";}}
# ------------------------------
# NOW we have all numbers to get
# sort the array
@wantNum= sort bynumber (@wantNum);
# too many wanted
if (defined @wantNum && ($wantNum[$#wantNum] > $locNum[$#locNum])){
$#tmp=0;
foreach $want (@wantNum){
if ($want <= $locNum[$#locNum]){
push(@tmp,$want)}
else {
print "-*- WARNING $sbrName no $want not in '$fileInLoc'\n";
exit;
}}
@wantNum=@tmp;}
@wantNum=@locNum if ($LreadAll);
if ($#wantNum==0){
print "*** ERROR $sbrName nothing to read ???\n";
return(0);}
# sort the array, again
@wantNum= sort bynumber (@wantNum);
# ------------------------------
# assign pointers to final output
foreach $it (1..$#wantNum){
$numWant=$wantNum[$it];
$ptr_numWant2numFin[$numWant]=$it;
$ptr_numFin2numWant[$it]= $numWant;}
# ------------------------------
# get blocks to take
$wantLast=$wantNum[$#wantNum];$#wantBlock=0;
foreach $ctBlock (1..$nmaxBlocks){
$beg=1+($ctBlock-1)*70;
$end=$ctBlock*70;
last if ($wantLast < $beg);
$Ltake=0;
foreach $num(@wantNum){
if ( ($beg<=$num)&&($num<=$end) ){
$Ltake=1;
last;}}
if ($Ltake){
$wantBlock[$ctBlock]=1;}
else{
$wantBlock[$ctBlock]=0;}}
# writes ids read
$tmp{"SWISS"}="";
foreach $it (1..$#wantNum){ $num=$wantNum[$it];
$tmp{$it}= $ptr_num2id[$num];
$tmp{"SWISS"}.=$ptr_num2id[$num].",";}
$tmp{"SWISS"}=~s/,*$//g;
$tmp{"NROWS"}=$#wantNum;
# ------------------------------------------------------------
#
# NOTATION:
# $tmp{"0",$it}= $it-th residue of guide sequnec
# $tmp{$itali,$it}= $it-th residue of of ali $itali
# note: itali= same numbering as in 1..$#want
# i.e. NOT the position in the file
# $ptr_numFin2numWant[$itali]=5 may reveal that
# the itali-th ali was actually the fifth in the
# HSSP file!!
#
# ------------------------------------------------------------
# --------------------------------------------------
# read the file finally
# --------------------------------------------------
$Lok=&open_file("$fhinLoc","$fileInLoc");
if (! $Lok){print "*** ERROR $sbrName opening hssp file '$fileInLoc'\n";
return(0);}
# ------------------------------
# move until first alis
# ------------------------------
$ctBlock=$Lread=$#takeTmp=0;
while (<$fhinLoc>){
last if ($_=~/$regexpEndAli/); # ending
if ($_=~/$regexpBegAli/){ # this block to take?
++$ctBlock;$Lread=0;
if ($wantBlock[$ctBlock]){
$_=~s/^[^0-9]+(\d+) -\s+(\d+).*$//;
$beg=$1;$end=$2;$Lread=1;
$#wantTmp=0; # local numbers
foreach $num (@wantNum){
if ( ($beg<=$num) && ($num<=$end) ){
$tmp=($num-$beg)+1;
print
"*** $sbrName negative number $tmp,$beg,$end,\n" x 3 if ($tmp<1);
push(@wantTmp,$tmp);}}
next;}}
next if (! $Lread); # move on
next if ($_=~/$regexpSkip/); # skip line
$line=$_;
# --------------------
if (length($line)<52){ # no alis in line
$seqNo=substr($line,1,6);$seqNo=~s/\s//g;
if (! defined $seqNo{$seqNo}){
$seqNo{$seqNo}=1;
push(@seqNo,$seqNo);}
# NOTE: $chn,$sec,$acc are returned per residue!
if (! defined $tmp{"0","$seqNo"}){
($seqNo,$pdbNo,
$tmp{"chn","$seqNo"},$tmp{"0","$seqNo"},
$tmp{"sec","$seqNo"},$tmp{"acc","$seqNo"})=
&hsspRdSeqSecAccOneLine($line);}
foreach $num(@wantTmp){ # add insertions if no alis
$pos= $num+$beg-1;
$posFin= $ptr_numWant2numFin[$pos];
$tmp{"$posFin","$seqNo"}="."; }
next;}
# ------------------------------
# everything fine, so read !
# ------------------------------
# --------------------
# first the HSSP stuff
$seqNo=substr($line,1,6);$seqNo=~s/\s//g;
if (! defined $seqNo{$seqNo}){
$seqNo{$seqNo}=1;
push(@seqNo,$seqNo);}
# NOTE: $chn,$sec,$acc are returned per residue!
if (! defined $tmp{"0","$seqNo"}){
($seqNo,$pdbNo,
$tmp{"chn","$seqNo"},$tmp{"0","$seqNo"},
$tmp{"sec","$seqNo"},$tmp{"acc","$seqNo"})=
&hsspRdSeqSecAccOneLine($line);}
# --------------------
# now the alignments
$alis=substr($line,52); $alis=~s/\n//g;
# NOTE: @wantTmp has the positions to read in current block,
# e.g. want no 75, block=71-90, => 75->4
foreach $num (@wantTmp){
$pos= $num+$beg-1; # note: beg=71 in the example above
$id= $ptr_num2id[$pos];
$posFin= $ptr_numWant2numFin[$pos];
$tmp{"$posFin"}= $id;
$takeTmp[$pos]= 1;
print "*** $sbrName neg number $pos,$beg,$num,\n" x 3 if ($pos<1);
$tmp{"seq","$posFin"}= "" if (! defined $tmp{"seq","$posFin"});
if (length($alis) < $num){
$tmp{"seq","$posFin"}.= ".";
$tmp{"$posFin","$seqNo"}=".";}
else {
$tmp{"seq","$posFin"}.= substr($alis,$num,1);
$tmp{"$posFin","$seqNo"}=substr($alis,$num,1);}}}
# ------------------------------
while (<$fhinLoc>){ # skip over profiles
last if ($_=~/$regexpBegIns/); } # begin reading insertion list
# ----------------------------------------
# store sequences without insertions!!
# ----------------------------------------
if (defined $kwd{"seqNoins"} && $kwd{"seqNoins"}){
# --------------------
$seq=""; # guide sequence
foreach $seqNo(@seqNo){
$seq.=$tmp{"0","$seqNo"};}
$seq=~s/[a-z]/C/g; # small caps to 'C'
$tmp{"seqNoins","0"}=$seq;
# --------------------
# all others (by final count!)
foreach $it (1..$#wantNum){
$seq="";
foreach $seqNo(@seqNo){
$seq.=$tmp{$it,"$seqNo"};}
$seq=~s/\s/\./g; # fill up insertions
$seq=~tr/[a-z]/[A-Z]/; # small caps to large
$tmp{"seqNoins",$it}=$seq;}
}
# --------------------------------------------------
# read insertion list
#
# syntax of insertion list:
# ....,....1....,....2....,....3....,....4
# AliNo IPOS JPOS Len Sequence
# 9 58 59 5 kQLGAEi
#
# --------------------------------------------------
undef @insMax; # note: $insMax[$seqNo]=5 means at residue 'seqNo'
foreach $seqNo (@seqNo){ # the longest insertion was 5 residues
$insMax[$seqNo]=0;}
while (<$fhinLoc>){
$rd=$_;
last if ((! defined $kwd{"seqAli"} || ! $kwd{"seqAli"}) &&
(! defined $kwd{"seq"} || ! $kwd{"seq"}) );
next if ($rd =~ /AliNo\s+IPOS/); # skip key
last if ($rd =~ /^\//); # end
next if ($rd !~ /^\s*\d+/); # should not happen (see syntax)
$rd=~s/\n//g; $line=$rd;
$posIns=$rd; # current insertion from ali $pos
$posIns=~s/^\s*(\d+).*$/$1/;
# takeTmp[$pos]=1 if $pos to be read
next if (! defined $takeTmp[$posIns] || ! $takeTmp[$posIns]);
# ok -> take
$line=~s/^\s*|\s*$//g; # purge leading blanks
@tmp=split(/\s+/,$line);
$iposIns=$tmp[2]; # residue position of insertion
$seqIns= $tmp[5]; # sequence at insertion 'kQLGAEi'
$nresIns=(length($seqIns) - 2); # number of residues inserted
$posFin= $ptr_numWant2numFin[$posIns];
# --------------------------------------------------
# NOTE: here $tmp{$it,"$seqNo"} gets more than
# one residue assigned (ref=11)
# --------------------------------------------------
# change 'ACinK' -> 'ACINEWNK'
$tmp{"$posFin","$iposIns"}=substr($seqIns,1,(length($seqIns)-1));
# maximal number of insertions
$insMax[$iposIns]=$nresIns if ($nresIns > $insMax[$iposIns]);
} close($fhinLoc);
# end of reading file
# --------------------------------------------------
# ------------------------------
# final sequences (not aligned)
# ------------------------------
if (defined $kwd{"seq"} && $kwd{"seq"}){
foreach $it (0..$tmp{"NROWS"}){
$seq="";
foreach $seqNo(@seqNo){
$seq.=$tmp{$it,"$seqNo"};}
$seq=~s/[\s\.!]//g; # replace insertions
$seq=~tr/[a-z]/[A-Z]/; # all capitals
$tmp{"seq",$it}=$seq; }}
# ------------------------------
# fill up insertions
# ------------------------------
if (defined $kwd{"seqAli"} && $kwd{"seqAli"}){
undef %ali; # temporary for storing sequences
foreach $it (0..$tmp{"NROWS"}){
$ali{$it}="";} # set for all alis
# ------------------------------
foreach $seqNo(@seqNo){ # loop over residues
$insMax=$insMax[$seqNo];
# loop over all alis
foreach $it (0..$tmp{"NROWS"}){
# (1) CASE: no insertion
if ($insMax==0){
$ali{$it}.=$tmp{$it,"$seqNo"};
next;}
# (2) CASE: insertions
$seqHere=$tmp{$it,"$seqNo"};
$insHere=(1+$insMax-length($seqHere));
# NOTE: dirty fill them in 'somewhere'
# take first residue
$ali{$it}.=substr($seqHere,1,1);
# fill up with dots
$ali{$it}.="." x $insHere ;
# take remaining residues (if any)
$ali{$it}.=substr($seqHere,2) if (length($seqHere)>1); }}
# ------------------------------
# now assign to final
foreach $it (0..$tmp{"NROWS"}){
$ali{$it}=~s/\s/\./g; # replace ' ' -> '.'
$ali{$it}=~tr/[a-z]/[A-Z]/; # all capital
$tmp{"seqAli",$it}=$ali{$it};}
undef %ali; # slim-is-in!
}
# ------------------------------
# save memory
foreach $it (0..$tmp{"NROWS"}){
if ($it == 0){ # guide
$id= $idGuide; }
else { # pairs
$posOriginal=$ptr_numFin2numWant[$it];
$id= $ptr_num2id[$posOriginal]; }
$tmp{"$id"}= $id;
foreach $seqNo (@seqNo){
undef $tmp{$it,"$seqNo"};}}
undef @seqNo; undef %seqNo; undef @takeTmp; undef @idLoc;
undef @want; undef @wantNum; undef @wantId; undef @wantBlock;
undef %rdHeader; undef %ptr_id2num; undef @ptr_num2id;
undef @ptr_numWant2numFin; undef @ptr_numFin2numWant;
return(1,%tmp);
} # end of hsspRdAli
#==============================================================================
sub hsspRdHeader {
local ($fileInLoc,@kwdInLoc) = @_ ;
local ($sbrName,$fhinLoc,$tmp,
@kwdDefHsspTopLoc,@kwdDefHsspHdrLoc,@kwdHsspTopLoc,@kwdHsspHdrLoc,@tmp,
$regexpBegHeader,$regexpEndHeader,$regexpLongId,$lenStrid,$LisLongId,
%ptr,$kwd,$Lok,$Lpdb,$des,$beg,$end,$mid,$ct,$id,$strid,$ptr,$tmp);
$[ =1 ;
#-------------------------------------------------------------------------------
# hsspRdHeader reads a HSSP header
# in: $fileHssp (must exist),
# @kwdInLoc = one of the default keywords
# (@kwdLocHsspTop,@kwdLocHsspHeader)
# in: 'nopair' surpresses reading of pair information
# out: for top (e.g. NALIGN): $rd{"kwd"}
# for prot (e.g. LALI): $rd{"kwd",$it}
# note: for the later number of elements (it) in
# $rd{"NROWS"}
# special ID=ID1, $rd{"kwd",$it} existes for ID1 and ID2
#-------------------------------------------------------------------------------
$sbrName="lib-br:hsspRdHeader";$fhinLoc="FHIN"."$sbrName";$fhinLoc=~tr/[a-z]/[A-Z]/;
# file existing?
if (! -e $fileInLoc || ! &is_hssp($fileInLoc) ){
print "*** ERROR $sbrName no HSSP file '$fileInLoc'\n";
return(0);}
# ------------------------------
# settings describing format
@kwdDefHsspTopLoc= ("PDBID","DATE","SEQBASE","PARAMETER","THRESHOLD",
"REFERENCE","HEADER","COMPND","SOURCE","AUTHOR",
"SEQLENGTH","NCHAIN","KCHAIN","NALIGN");
@kwdDefHsspHdrLoc= ("NR","ID","STRID","IDE","WSIM","IFIR","ILAS",
"JFIR","JLAS","LALI","NGAP","LGAP","LSEQ2","ACCNUM","PROTEIN");
$regexpBegHeader= "^\#\# PROTEINS"; # begin of reading
$regexpEndHeader= "^\#\# ALIGNMENTS"; # end of reading
$regexpLongId= "^PARAMETER LONG-ID :YES"; # identification of long id
$lenStrid= 4; # minimal length to identify PDB identifiers
$LisLongId= 0; # long identifier names
$ptr{"IDE"}=1;$ptr{"WSIM"}=2;$ptr{"IFIR"}=3;$ptr{"ILAS"}=4;$ptr{"JFIR"}=5;$ptr{"JLAS"}=6;
$ptr{"LALI"}=7;$ptr{"NGAP"}=8;$ptr{"LGAP"}=9;$ptr{"LSEQ2"}=10; $ptr{"ACCNUM"}=11;
# ------------------------------
# check input arguments
$#kwdHsspTopLoc=$#kwdHsspHdrLoc=$Lpdb=$LnoPair=0;
foreach $kwd (@kwdInLoc){
$Lok=0;
if ($kwd eq "nopair"){
$LnoPair=1;
next;}
$Lpdb=1 if (! $Lpdb && ($kwd =~/^PDBID/));
foreach $des (@kwdDefHsspTopLoc) {
if ($kwd eq $des){ $Lok=1; push(@kwdHsspTopLoc,$kwd);
last;}}
next if ($Lok || $LnoPair);
foreach $des (@kwdDefHsspHdrLoc){
if ($kwd eq $des){ $Lok=1; push(@kwdHsspHdrLoc,$kwd);
last;} }
print "-*- WARNING $sbrName input kwd=$kwd, makes no sense??\n" if (! $Lok);}
# force reading of NALI
push(@kwdHsspTopLoc,"PDBID") if (! $Lpdb);
# get column numbers to read
# ------------------------------
# now start to read
$Lok=&open_file("$fhinLoc","$fileInLoc");
if (! $Lok){print "*** ERROR $sbrName HSSP file could not be opened '$fileInLoc'\n";
return(0);}
undef %tmp; # save space
# ------------------------------
while ( <$fhinLoc> ) { # read top
last if ($_ =~ /$regexpBegHeader/);
if ($_ =~ /$regexpLongId/) {
$LisLongId=1;}
else{$_=~s/\n//g;$arg=$_;
foreach $des (@kwdHsspTopLoc){
if ($arg =~ /^$des\s+(.+)$/){
if (defined $ok{"$des"}){ # multiple lines!
$tmp="$1"."\t";
if (defined $tmp{"$des"}){
$tmp{"$des"}.=$tmp;}
else{$tmp{"$des"}=$tmp;}}
else {$ok{"$des"}=1;$tmp{"$des"}=$1;}
if ($des=~/SEQLENGTH|NCHAIN|KCHAIN|NALIGN/){
$tmp{"$des"}=~s/^(\d+)[^0-9]+.*$/$1/;} # purge blanks
last;}}}}
# ------------------------------
$ct=0; # read header
while ( <$fhinLoc> ) {
last if ($LnoPair); # supress reading pair info
last if ($_ =~ /$regexpEndHeader/);
next if ($_ =~ /^ NR\./); # skip descriptors
$_=~s/\n//g;
$lenLine=length($_);
if ($LisLongId){
$maxMid=115; $maxMid=($lenLine-56) if ($lenLine < 115);
$maxEnd=109; $maxEnd=$lenLine if ($lenLine < 109);
$beg=substr($_,1,56);
$end=0; $end=substr($_,109) if ($lenLine >=109);
$mid=substr($_,57,115); }
else {
$maxMid= 62; $maxMid=($lenLine-28) if ($lenLine < 90);
$beg=substr($_,1,28);
$end=0; $end=substr($_,90) if ($lenLine >=90);
$mid=substr($_,29,90); }
$end=~s/^\s*|\s*$//g; # purge leading blanks
$mid=~s/^\s*|\s*$//g; # purge leading blanks
# SWISS accession: hack because it may be empty!
if ($lenLine > 86) {
$accnum=substr($_,81,6); $accnum=~s/(\s)\s+/$1/g ; }
else {
$accnum=0;}
# begin: counter and id
$beg=~s/.+ \:\s*|\s*$//g;
if (! $LisLongId) {$id=$beg;$id=~s/([^\s]+).*$/$1/;
$strid=$beg;$strid=~s/$id|\s//g; }
else {$id=$beg;$id=~s/(.+_\S+).*/$1/;
$strid=substr($_,49,6);$strid=~s/\s//g; }
$tmp=$lenStrid-1;
if ( (length($strid)<$lenStrid) && ($id=~/^[0-9][A-Z0-9]{$tmp,$tmp}\s*/)){
$strid=substr($id,1,$lenStrid); }
++$ct;
$tmp{"ID",$ct}= $id;
$tmp{"NR",$ct}= $ct;
$tmp{"STRID",$ct}= $strid;
# correct for ID = PDBid
$tmp{"STRID",$ct}= $id if ($strid=~/^\s*$/ && &is_pdbid($id));
$tmp{"PROTEIN",$ct}=$end;
$tmp{"ID1",$ct}=$tmp{"PDBID"};
$tmp{"ACCNUM",$ct}=$accnum;
# middle all info
$#tmp=0;@tmp=split(/\s+/,$mid);
foreach $_ (@tmp) {$_=~s/\s//g;}
foreach $des (@kwdHsspHdrLoc){
next if ( ! defined $ptr{"$des"});
next if ( $des =~/^ACCNUM/);
$ptr=$ptr{"$des"};
$tmp{"$des",$ct}=$tmp[$ptr]; }}close($fhinLoc);
$tmp{"NROWS"}=$ct;
# clean up
$#kwdInLoc=$#kwdDefHsspHdrLoc=$#kwdHsspTopLoc=$#tmp=
$#kwdDefHsspTopLoc=$#kwdHsspHdrLoc=0;
undef %ptr;
return(1,%tmp);
} # end of hsspRdHeader
#==============================================================================
sub hsspRdSeqSecAccOneLine {
local ($inLine) = @_ ;
local ($sbrName,$fhinLoc,$seqNo,$pdbNo,$chn,$seq,$sec,$acc,$tmp);
$[ =1 ;
#-------------------------------------------------------------------------------
# hsspRdSeqSecAccOneLine reads begin of one HSSP line
#-------------------------------------------------------------------------------
$sbrName="hsspRdSeqSecAccOneLine";
$seqNo=substr($inLine,1,6);$seqNo=~s/\s//g;
$pdbNo=substr($inLine,7,5);$pdbNo=~s/\s//g;
$chn= substr($inLine,13,1);
$seq= substr($inLine,15,1);
$sec= substr($inLine,18,1);
$acc= substr($inLine,36,4);$acc=~s/\s//g;
return($seqNo,$pdbNo,$chn,$seq,$sec,$acc)
} # end of hsspRdSeqSecAccOneLine
#==============================================================================
sub isDaf {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isDaf checks whether or not file is in DAF format
# (i.e. the dirty ali format used for aqua)
# in: $file
# out: 1 if is DAF; 0 else
#--------------------------------------------------------------------------------
open("FHIN_DAF","$fileLoc") || Carp::confess( "failed to open $fileLoc: $!" );
while (<FHIN_DAF>){ if ($_=~/^\# DAF/){$Lok=1;}
else {$Lok=0;}
last;}close(FHIN_DAF);
return($Lok);
} # end of isDaf
#===============================================================================
sub isFasta {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isFasta checks whether or not file is in FASTA format
# (first line /^>\w/, second (non white) = AA
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
$fhinLoc2="FHIN_FASTA";
open($fhinLoc2,$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" );
$one=(<$fhinLoc2>);
$two=(<$fhinLoc2>);
$two=~s/\s|\n//g if (defined $two);
close($fhinLoc2);
return(0) if (! defined $two || ! defined $one);
return(1) if ($one =~ /^\s*>\s*\w+/ &&
$two !~ /[^A-Z.~_!-]/io);
return(0);
} # end of isFasta
#==============================================================================
sub isFastaMul {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isFastaMul checks whether more than 1 sequence in FASTA found
# (first line /^>\w/, second (non white) = AA *2
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
$fhinLoc2="FHIN_FASTA";
open($fhinLoc2,$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return(0);
$one=(<$fhinLoc2>);
$two=(<$fhinLoc2>);
$two=~s/\s//g if (defined $two);
return (0) if (! defined $two || ! defined $one);
return (0) if (($one !~ /^\s*\>\s*\w+/) ||
($two =~ /[^A-Z.~_!-]/io));
$Lok=0;
while (<$fhinLoc2>) {
next if ($_ !~ /^\s*>\s*\w+/);
$Lok=1;
last;}close($fhinLoc2);
return($Lok);
} # end of isFastaMul
#==============================================================================
sub isGcg {
local ($fileLoc) = @_ ; $[ =1 ;
#--------------------------------------------------------------------------------
# isGcg checks whether or not file is in Gcg format (/# SAF/)
# in: $file
# out: 1 if is yes; 0 else
# EXA: paho_chick from: 1 to: 80
# EXA: PANCREATIC HORMONE PRECURSOR (PANCREATIC POLYPEPTIDE) (PP).
# EXA: paho_chick.gcg Length: 80 31-May-98 Check: 8929 ..
# EXA: 1 MPPRWASLLL LACSLLLLAV PPGTAGPSQP TYPGDDAPVE DLIRFYNDLQ
# EXA: 51 QYLNVVTRHR YGRRSSSRVL CEEPMGAAGC
#--------------------------------------------------------------------------------
return(0) if (! defined $fileLoc || ! -e $fileLoc);
$fhinLoc="FHIN_GCG";
open($fhinLoc,$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || do { cluck "-*- isGcg failed opening=$fileLoc\n";
return(0); };
$ctLocFlag=$#tmp=0;
while(<$fhinLoc>){++$ctLocFlag;
push(@tmp,$_);
last if ($ctLocFlag==5);}
close($fhinLoc);
$ctLocFlag=$already_sequence=0;
foreach $tmp (@tmp){
last if ($tmp=~/^\#/); # avoid being too friendly to GCG!
if ($tmp=~/from\s*:\s*\d+\s*to:\s*\d+/i) {
++$ctLocFlag;}
elsif($tmp=~/^\s*\w+\s+Length\s*:\s+\d+\s+\d\d\-/i) {
++$ctLocFlag;}
elsif(! $already_sequence && $tmp=~/[\s\t]*\d+\s+[A-Z]+/i) {
$already_sequence=1;
++$ctLocFlag;}
last if ($ctLocFlag==3);}
return(1) if ($ctLocFlag==3);
return(0) ;
} # end of isGcg
#==============================================================================
sub isMsf {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isMsf checks whether or not file is in MSF format
# (i.e. the dirty ali format used for aqua)
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
open("FHIN_MSF","$fileLoc") || Carp::confess( "failed to open $fileLoc: $!" );
$ct=0;
while (<FHIN_MSF>){ $Lok=0;
$Lok=1 if ($_=~/\s*MSF[\s:]+/ ||
# new PileUp shit
$_=~/\s*PileUp|^\s*\!\!AA_MULTIPLE_ALIGNMENT/);
last;}
close(FHIN_MSF);
return($Lok);
} # end of isMsf
#===============================================================================
sub isPdb {
local ($fileLoc) = @_ ; local ($Lok,$fhinLoc,$fileTmp);
#--------------------------------------------------------------------------------
# isPdb checks whether or not file is PDB format
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
$fhinLoc="FhIn_PDB";$Lok=0;
open($fhinLoc,$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) ||
do { cluck "*** isPdb failed opening file=$fileLoc!\n";
return(0); };
$tmp="";
while(<$fhinLoc>){
$tmp=$_; $tmp=~s/\n//g;
last;}
close($fhinLoc);
#HEADER PANCREATIC HORMONE 16-JAN-81 1PPT 1PPT 3
return(1)
if ($tmp=~/^HEADER\s+.*\d\w\w\w\s+\d+\s*$/);
return(0);
} # end of isPdb
#==============================================================================
sub isPhdAcc {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isPhdAcc checks whether or not file is in PHD.rdb_acc format
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
open("FHIN_RDB_PHDACC",$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return(0);
$ctLoc=0;
while (<FHIN_RDB_PHDACC>){
$_=~s/^[\#\s]//g;
next if (length($_)<5);
++$ctLoc;
last if ($ctLoc>3);
if ($ctLoc==1 && $_=~/^\s*Perl-RDB/){
$Lok=1;}
elsif ($ctLoc==1) {
close(FHIN_RDB_PHDACC);
return(0);}
elsif ($_=~/PHDacc/) {
close(FHIN_RDB_PHDACC);
return(1);}}
close(FHIN_RDB_PHDACC);
return(0);
} # end of isPhdAcc
#===============================================================================
sub isPhdBoth {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isPhdBoth checks whether or not file is in PHD.rdb format
# acc + sec
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
open("FHIN_RDB_PHDBOTH",$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return(0);
$ctLoc=0;
while (<FHIN_RDB_PHDBOTH>){
$_=~s/^[\#\s]//g;
next if (length($_)<5);
++$ctLoc;
last if ($ctLoc>3);
if ($ctLoc==1 && $_=~/^\s*Perl-RDB/) {
$Lok=1;}
elsif ($ctLoc==1) {
close(FHIN_RDB_PHDBOTH);
return(0); }
elsif ($_=~/PHDsec/ && $_=~/PHDacc/) {
close(FHIN_RDB_PHDBOTH);
return(1);}}
close(FHIN_RDB_PHDBOTH);
return(0);
} # end of isPhdBoth
#==============================================================================
sub isPhdHtm {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isPhdHtm checks whether or not file is in PHD.rdb_htm format
# (i.e. the dirty ali format used for aqua)
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
open("FHIN_RDB_PHDHTM",$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return(0);
$ctLoc=0;
while (<FHIN_RDB_PHDHTM>){
$_=~s/^[\#\s]//g;
next if (length($_)<5);
++$ctLoc;
last if ($ctLoc>3);
if ($ctLoc==1 && $_=~/^\s*Perl-RDB/){
$Lok=1;}
elsif ($ctLoc==1) {
close(FHIN_RDB_PHDHTM);
return(0);}
elsif ($_=~/PHDhtm/){
close(FHIN_RDB_PHDHTM);
return(1);}}
close(FHIN_RDB_PHDHTM);
return(0);
} # end of isPhdHtm
#==============================================================================
sub isPhdSec {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isPhdSec checks whether or not file is in PHD.rdb_sec format
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
open("FHIN_RDB_PHDSEC",$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return(0);
$ctLoc=0;
while (<FHIN_RDB_PHDSEC>){
$_=~s/^[\#\s]//g;
next if (length($_)<5);
++$ctLoc;
last if ($ctLoc>3);
if ($ctLoc==1 && $_=~/^\s*Perl-RDB/) {
$Lok=1;}
elsif ($ctLoc==1) {
close(FHIN_RDB_PHDSEC);
return(0); }
elsif ($_=~/PHDsec/) {
close(FHIN_RDB_PHDSEC);
return(1);}}
close(FHIN_RDB_PHDSEC);
return(0);
} # end of isPhdSec
#==============================================================================
sub isPir {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isPir checks whether or not file is in Pir format
# (first line /^>P1\;/, second (non white) = AA
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
open("FHIN_PIR",$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return(0);
$one=(<FHIN_PIR>);close(FHIN_PIR);
return(1) if (defined $one && $one =~ /^\>P1\;/i);
return(0);
} # end of isPir
#==============================================================================
sub isPirMul {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isPirMul checks whether or not file contains many sequences
# in PIR format
# more than once: first line /^>P1\;/
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
open("FHIN_PIR",$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return(0);
$ctLoc=0;
while(<FHIN_PIR>){
++$ctLoc if ($_=~/^>P1\;/i);
last if ($ctLoc>1);}
close(FHIN_PIR);
return(1) if ($ctLoc>1);
return(0);
} # end of isPirMul
#==============================================================================
sub isRdb {
local ($fileInLoc) = @_ ;local ($fh);
#--------------------------------------------------------------------------------
# isRdb checks whether or not file is in RDB format
# in: file
# out: returns 1 if is RDB, 0 else
#--------------------------------------------------------------------------------
return (0) if (! -e $fileInLoc);
$fh="FHIN_CHECK_RDB";
open("$fh", $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$tmp=<$fh>;
close($fh);
return(1) if (defined $tmp && $tmp =~/^\# .*RDB/);
return 0;
} # end of isRdb
#==============================================================================
sub isSaf {
local ($fileLoc) = @_ ;
#--------------------------------------------------------------------------------
# isSaf checks whether or not file is in SAF format (/# SAF/)
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
return(0) if (! defined $fileLoc || ! -e $fileLoc);
$fhinLoc="FHIN_SAF";
open("$fhinLoc",$fileLoc) || Carp::confess( "failed to open $fileLoc: $!" ) || return (0);
$tmp=<$fhinLoc>;
close("$fhinLoc");
return(1) if (defined $tmp && $tmp =~ /^\#.*SAF/);
return(0);
} # end of isSaf
#==============================================================================
sub isSwiss {
local ($fileLoc) = @_ ; local ($Lok);
#--------------------------------------------------------------------------------
# isSwiss checks whether or not file is in SWISS-PROT format (/^ID /)
# in: $file
# out: 1 if is yes; 0 else
#--------------------------------------------------------------------------------
$fhinLoc="FHIN_SWISS";
open("$fhinLoc","$fileLoc") || Carp::confess( "failed to open $fileLoc: $!" ); $Lok=0;
while (<$fhinLoc>){
$Lok=1 if ($_=~/^ID /);
last;}
close($fhinLoc);
return($Lok);
} # end of isSwiss
#==============================================================================
sub is_chain {
local($tmp) = @_ ;
#-------------------------------------------------------------------------------
# is_chain checks whether or not a PDB chain
# in: character
# out: 1,0
#-------------------------------------------------------------------------------
return(0) if (! defined $tmp);
return(1) if ($tmp=~/[A-Z0-9]/);
return(0);
} # end of is_chain
#==============================================================================
sub is_dssp {
local ($fileInLoc) = @_ ;
local ($fh,$Lis);
#--------------------------------------------------------------------------------
# is_dssp checks whether or not file is in DSSP format
# in: $file
# out: 1 if is dssp; 0 else
#--------------------------------------------------------------------------------
return (0) if (! defined $fileInLoc || ! -e $fileInLoc);
$fh="FHIN_CHECK_DSSP";
open($fh,$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$Lis=0;
while ( <$fh> ) {
$Lis=1
if ($_=~/SECONDARY STRUCTURE DEFINITION BY THE PROGRAM DSSP/i);
last; }
close($fh);
return $Lis;
} # end of is_dssp
#==============================================================================
sub is_fssp {
local ($fileInLoc) = @_ ;
#--------------------------------------------------------------------------------
# is_fssp checks whether or not file is in FSSP format
# in: $file
# out: 1 if is fssp; 0 else
#--------------------------------------------------------------------------------
return(0) if (! defined $fileInLoc || ! -e $fileInLoc);
$fh="FHIN_CHECK_FSSP";
open($fh, $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$tmp=<$fh> ;
close($fh);
return(1) if (defined $tmp && $tmp=~/^FSSP/);
return(0);
} # end of is_fssp
#==============================================================================
sub is_hssp {
local ($fileInLoc) = @_ ;local ($fh,$Lis);
#--------------------------------------------------------------------------------
# is_hssp checks whether or not file is in HSSP format
# in: $file
# out: 1 if is hssp; 0 else
#--------------------------------------------------------------------------------
return (0) if (! defined $fileInLoc || ! -e $fileInLoc) ;
$fh="FHIN_CHECK_HSSP";
open($fh, $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$Lis=0;
while ( <$fh> ) {
$Lis=1 if (/^HSSP/) ;
last; }
close($fh);
return $Lis;
} # end of is_hssp
#==============================================================================
sub is_pdbid {
local ($id) = @_ ;
#--------------------------------------------------------------------------------
# is_pdbid checks whether or not id is a valid PDBid (number 3 char)
# in: $file
# out: 1 if is DBid, 0 else
#--------------------------------------------------------------------------------
return 1
if ((length($id) <= 6) &&
($id=~/^[0-9][0-9a-z]{3,3}[^0-9a-z]?/));
return 0;
} # end of is_pdbid
#==============================================================================
sub is_ppcol {
local ($fileInLoc) = @_ ;
local ($fh,$Lis);
#--------------------------------------------------------------------------------
# is_ppcol checks whether or not file is in RDB format
# in: $file
# out: 1 if is ppcol, 0 else
#--------------------------------------------------------------------------------
return(0) if (! defined $fileInLoc || ! -e $fileInLoc);
$fh="FHIN_CHECK_HSSP";
open($fh, $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" );
$Lis=0;
while ( <$fh> ) {
$_=~tr/[A-Z]/[a-z]/;
$Lis=1 if ($_=~/^\# pp.*col/);
last; }
close($fh);
return $Lis;
} # end of is_ppcol
#==============================================================================
sub is_rdb_htmref {
local ($fileInLoc) = @_ ;local ($fh,$Lisrdb,$Lishtm);
#--------------------------------------------------------------------------------
# is_rdb_htmref checks whether or not file is RDB from PHDhtm_ref
# in: $file
# out: 1 if is .; 0 else
#--------------------------------------------------------------------------------
return (0) if (! -e $fileInLoc);
$fh="FHIN_CHECK_RDB_PHDHTM_REF";$Lisrdb=$Lishtm=0;
open($fh, $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$ctLoc=$Lishtm=0;
while ( <$fh> ) {
++$ctLoc;
$Lisrdb=1 if ($_=~/^\# Perl-RDB/);
last if (! $Lisrdb);
$Lishtm=1 if ($_=~/^\#\s*PHD\s*htm.*ref\:/);
last if ($Lishtm);
last if ($_ !~/^\#/);
last if ($ctLoc > 5); }
close($fh);
return ($Lishtm);
} # end of is_rdb_htmref
#==============================================================================
sub is_rdb_htmtop {
local ($fileInLoc) = @_ ;local ($fh,$Lisrdb,$Lishtm);
#--------------------------------------------------------------------------------
# is_rdb_htmtop checks whether or not file is RDB from PHDhtm_top
# in: $file
# out: 1 if is .; 0 else
#--------------------------------------------------------------------------------
return (0) if (! -e $fileInLoc);
$fh="FHIN_CHECK_RDB_PHDHTM_TOP";$Lisrdb=$Lishtm=0;
open($fh, $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$ctLoc=$Lishtm=0;
while ( <$fh> ) {
++$ctLoc;
$Lisrdb=1 if ($_=~/^\# Perl-RDB/);
last if (! $Lisrdb);
$Lishtm=1 if ($_=~/^\#\s*PHD\s*htm.*top\:/);
last if ($Lishtm);
last if ($_ !~/^\#/);
last if ($ctLoc > 5); }
close($fh);
return ($Lishtm);
} # end of is_rdb_htmtop
#==============================================================================
sub is_rdb_nnDb {
local ($fileInLoc) = @_ ;
local ($fh,$Lisrdb,$Lisacc);
#--------------------------------------------------------------------------------
# is_rdb_nnDb checks whether or not file is in RDB format for NN.pl
# in: $file
# out: 1 if is rdb_nn; 0 else
#--------------------------------------------------------------------------------
return (0) if (! -e $fileInLoc);
$fh="FHIN_CHECK_RDB_RDBNN";
open($fh, $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$tmp=(<$fh>);
close($fh);
return(1) if (defined $tmp && $tmp=~/^\# Perl-RDB.*NNdb/i);
return (0);
} # end of is_rdb_nnDb
#==============================================================================
sub is_strip {
local ($fileInLoc) = @_ ;
local ($fh,$Lis);
#--------------------------------------------------------------------------------
# is_strip checks whether or not file is in HSSP-strip format
# in: $file
# out: 1 if is strip; 0 else
#--------------------------------------------------------------------------------
return (0) if (! -e $fileInLoc);
$fh="FHIN_CHECK_STRIP";
open($fh, $fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(0);
$Lis=0;
while ( <$fh> ) {
$Lis=1 if ($_=~/=== MAXHOM-STRIP ===/);
last; }
close($fh);
return $Lis;
} # end of is_strip
#==============================================================================
sub msfBlowUp {
local($fileInLoc,$fileOutLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# msfBlowUp duplicates guide sequence for conversion to HSSP
# in: $fileInLoc,$fileOutLoc
# out: 1|0, msg,
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."msfBlowUp";
$fhinLoc="FHIN_"."msfBlowUp";$fhoutLoc="FHOUT_"."msfBlowUp";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
($Lok,$msg,%msfIn)=&msfRd($fileInLoc);
return(0,"*** ERROR $sbrName: msfRd \n".$msg."\n") if (! $Lok);
open("$fhoutLoc",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(0,"*** ERROR $sbrName: fileNew=$fileOutLoc, not opened\n");
$name=$msfIn{"id","1"};
$namex=substr($name,1,(length($name)-1))."x";
$namex.="x" if ($name eq $namex);
$tmp{"1"}=$name;
$tmp{"2"}=$namex;
$tmp{SEQS}->{$name}= $msfIn{"seq","1"};
$tmp{SEQS}->{$namex}= $msfIn{"seq","1"};
$tmp{"NROWS"}= 2;
$tmp{"FROM"}= $fileInLoc;
$tmp{"TO"}= $fileOutLoc;
undef %msfIn; # save memory
# write msf
open ("$fhoutLoc",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(0,"*** ERROR $sbrName: failed opening new '$fileOutLoc'\n") ;
($Lok,$msg)=
&msfWrt($fhoutLoc,%tmp);
close($fhoutLoc);
return(0,"*** ERROR $sbrName: failed to write $fileOutLoc, \n".$msg."\n")
if (! $Lok || ! -e $fileOutLoc);
return(1,"ok $sbrName");
} # end of msfBlowUp
#==============================================================================
sub msfCheckFormat {
local ($fileMsf) = @_;
local ($format,$tmp,$kw_msf,$kw_check,$ali_sec,$ali_des_sec,$valid_id_len,$fhLoc,
$uniq_id, $same_nb, $same_len, $nb_al, $seq_tmp, $seql, $ali_des_len);
$[ =1 ;
#--------------------------------------------------------------------------------
# msfCheckFormat basic checking of msf file format
# - mandatory keywords and values (MSF: val, Check: val)
# - alignment description start after "..", each line with the following structure:
# Name: id Len: val Check: val Weight: val (and all ids diferents)
# - alignment same number of line for each id (>0)
# in: $fileMsf
# out: return 1 if format seems OK, 0 else
#--------------------------------------------------------------------------------
$sbrNameLoc="msfCheckFormat";
# ----------------------------------------
# initialise the flags
# ----------------------------------------
$fhLoc="FHIN_CHECK_MSF_FORMAT";
$kw_msf=$kw_check=$ali_sec=$ali_des_sec=$ali_des_seq=$nb_al=0;
$format=1;
$valid_id_len=1; # sequence name < 15 characters
$uniq_id=1; # id must be unique
$same_len=1; # each seq must have the same len
$lenok=1; # length in header and of sequence differ
# ----------------------------------------
# read the file
# ----------------------------------------
open ($fhLoc,$fileMsf) || Carp::confess( "failed to open $fileMsf: $!" ) ||
return(0,"*** $sbrNameLoc cannot open fileMsf=$fileMsf\n");
while (<$fhLoc>) {
$_=~s/\n//g;
$tmp=$_;$tmp=~ tr/a-z/A-Z/;
# MSF keyword and value
$kw_msf=1 if (!$ali_des_seq && ($tmp =~ /MSF:\s*\d*\s/));
next if (!$kw_msf);
# CHECK keyword and value
$kw_check=1 if (!$ali_des_seq && ($tmp =~ /CHECK:\s*\d*/));
next if (!$kw_check);
# begin of the alignment description section
# the line with MSF and CHECK must end with ".."
if (!$ali_sec && $tmp =~ /MSF:\D*(\d*).*CHECK:.*\.\.\s*$/) {
$ali_des_len=$1;$ali_des_sec=1;}
# ------------------------------
# the alignment description section
if (!$ali_sec && $ali_des_sec) {
if ($tmp=~ /^\s*NAME:\s*(\S*).*LEN:.*\d.*CHECK:.*\d.*WEIGHT:.*\d.*/) {
$id=$1;
$valid_id_len=0 if (length($id) > 14); # is sequence name <= 14
if ($SEQID{$id}) { # is the sequence unique?
$uniq_id=0; $ali_sec=1;
last; }
$lenRd=$tmp;$lenRd=~s/^.*LEN\:\s*(\d+)\s*CHEC.*$/$1/;
$SEQID{$id}=1; # store seq ID
$SEQL{$id}= 0; # initialise seq len array
} }
# ------------------------------
# begin of the alignment section
$ali_sec=1 if ($ali_des_sec && $tmp =~ /\/\/\s*$/);
# ------------------------------
# the alignment section
if ($ali_sec) {
if ($tmp =~ /^\s*(\S+)\s+(.*)$/) {
$id= $1;
if ($SEQID{$id}) {++$SEQID{$id};
$seq_tmp= $2;$seq_tmp=~ s/\s|\n//g;
$SEQL{$id}+= length($seq_tmp);}}}
}close($fhLoc);
# ----------------------------------------
# test if all sequences are present the
# same number of time with the same length
# ----------------------------------------
if ($kw_msf && $kw_check && $ali_des_sec && $uniq_id && $valid_id_len){
foreach $id (keys %SEQID) {
$nb_al= $SEQID{$id} if (!$nb_al);
if ($SEQID{$id} < 2 || $SEQID{$id} != $nb_al) {
$same_len=0;
last; }
if ($SEQL{$id} != $lenRd){
$lenok=0;
last;}}}
# TEST ALL THE FLAGS
$msg="";
$msg.="*** $sbrNameLoc wrong MSF: no keyword MSF!\n" if (!$kw_msf);
$msg.="*** $sbrNameLoc wrong MSF: no keyword Check!\n" if (!$kw_check);
$msg.="*** $sbrNameLoc wrong MSF: no ali descr section!\n" if (!$ali_des_sec);
$msg.="*** $sbrNameLoc wrong MSF: no ali section!\n" if (!$ali_sec);
$msg.="*** $sbrNameLoc wrong MSF: id not unique!\n" if (!$uniq_id);
$msg.="*** $sbrNameLoc wrong MSF: seq name too long!\n" if (!$valid_id_len);
$msg.="*** $sbrNameLoc wrong MSF: varying length of seq!\n" if (!$same_len);
$msg.="*** $sbrNameLoc wrong MSF: length given and real differ!\n" if (!$lenok);
return(0,$msg) if (length($msg)>1);
return(1,"$sbrNameLoc ok");
} # end msfCheckFormat
#===============================================================================
sub msfCompress {
local($fileInLoc,$fileOutLoc) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# msfCompress deletes insertions in guide sequence
# in: $fileInLoc
# out: 1|0,msg, implicit:
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."msfCompress";
$fhinLoc="FHIN_"."msfCompress";$fhoutLoc="FHOUT_"."msfCompress";
# check arguments
return(&errSbr("not def fileInLoc!")) if (! defined $fileInLoc);
return(&errSbr("not def fileOutLoc!")) if (! defined $fileOutLoc);
return(&errSbr("no fileIn=$fileInLoc!")) if (! -e $fileInLoc);
# number of characters per line
$nperlineLoc=60;
# open MSF file
open($fhinLoc,$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(&errSbr("fileInLoc=$fileInLoc, not opened"));
$#tmp=0;
undef %msfIn; # ------------------------------
while (<$fhinLoc>) { # read file
$_=~s/\n//g;
push(@tmp,$_);
last if ($_ eq "//" ); # skip everything before ali sections
}
undef %tmp;$ct=0;
while (<$fhinLoc>) { # read file
$_=~s/\n//g;
$_=~s/^\s*|\s*$//g; # purge leading blanks
$rd=$_;
$tmp=$_;
$tmp=~s/^\s*\d+[\s\t\.\,\d]+$//g;
next if (length($tmp)<1); # skip lines empty or with numbers, only
# --------------------
# from here on: 'id sequence'
$id= $rd; $id =~s/^\s*(\S+)\s*.*$/$1/;
$seq=$rd; $seq=~s/^\s*(\S+)\s+(\S.*)$/$2/;
$seq=~s/\s//g;
if (! defined $tmp{$id}){ # new
++$ct;$tmp{$id}=$ct;
$msfIn{"id",$ct}= $id;
$msfIn{"seq",$ct}=$seq;}
else {
$ptr=$tmp{$id};
$msfIn{"seq",$ptr}.=$seq;
}
}
close($fhinLoc);
$msfIn{"NROWS"}=$ct;
# ------------------------------
# now compress insertions in guide
# ------------------------------
$ctcleave=$ctres=0;
$lenloc=length($msfIn{"seq",1});
# all 0
foreach $itprot (1..$msfIn{"NROWS"}){
$msfIn{"new",$itprot}="";
}
# loop over all residues
foreach $itres (1..$lenloc){
# is residue
if (substr($msfIn{"seq",1},$itres,1)=~/^[A-Za-z]/){
foreach $itprot (1..$msfIn{"NROWS"}){
$msfIn{"new",$itprot}.=substr($msfIn{"seq",$itprot},$itres,1);
}
++$ctres;
next;}
# seems insertion
++$ctcleave;
}
# check: sum ok?
return(0,"*** $sbrName: failed at compressing ncleave=$ctcleave, nresnew=$ctres,".
" before=".$lenloc." file=$fileInLoc!")
if ($lenloc != ($ctcleave + $ctres));
# replace by cleaved version
foreach $itprot (1..$msfIn{"NROWS"}){
$msfIn{"seq",$itprot}=$msfIn{"new",$itprot};
}
# ------------------------------
# write new MSF
# ------------------------------
open($fhoutLoc,">".$fileOutLoc) || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(&errSbr("fileOutLoc=$fileOutLoc, not created"));
# get longest name
$maxlen=0;
foreach $itprot (1..$msfIn{"NROWS"}){
$maxlen=length($msfIn{"id",$itprot}) if (length($msfIn{"id",$itprot}) > $maxlen);
}
# header
foreach $tmp (@tmp){
$tmp=~s/$lenloc/$ctres/g; # replace old by new length
print $fhoutLoc $tmp,"\n";
}
# body
for($it=1;$it<=$ctres;$it+=$nperlineLoc){
print $fhoutLoc
"\n";
printf $fhoutLoc
"%-".$maxlen."s %-s\n",
" ",$it." " x ($nperlineLoc-length($it)-length($it+$nperlineLoc)) .($it+$nperlineLoc);
foreach $itprot (1..$msfIn{"NROWS"}){
printf $fhoutLoc
"%-".$maxlen."s %-s\n",
$msfIn{"id",$itprot},substr($msfIn{"seq",$itprot},$it,$nperlineLoc),"\n";
}
}
close($fhoutLoc);
return(0,"*** $sbrName: no output file=$fileOutLoc!")
if (! -e $fileOutLoc);
# clean up
undef %msfIn; undef %tmp; # slim-is-in
$#tmp=0;
return(1,"ok $sbrName");
} # end of msfCompress
#==============================================================================
sub msfCountNali {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# msfCountNali counts the number of alignments in MSF file
# in: file
# out: $nali,$msg if error
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName="$tmp"."msfCountNali";$fhinLoc="FHIN_"."msfCountNali";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
open("$fhinLoc","<", $fileInLoc) || do {
Carp::confess( "failed to open <$fileInLoc: $!" );
return(0,"*** ERROR $sbrName: fileIn=$fileInLoc, not opened\n");
};
$ct=0; # ------------------------------
while (<$fhinLoc>) { # read MSF
chomp;
#Name: tsnap Len: 332 Check: 2222 Weight: 1.00
if($_=~ /^\s*NAME:\s*(\S+).*LEN:.*\d+\s*CHECK:\s*\d+\s*WEIGHT:/i){ ++$ct; }
last if ($_ eq "//" );
next;} close($fhinLoc);
return($ct);
} # end of msfCountNali
#==============================================================================
sub msfRd {
local ($fileInLoc) = @_ ;
local ($sbrName,$Lok,$msg,$tmp,$fhout,$LfirstLine,$Lhead,
$Lguide,$seqGuide,$nameGuide);
$[ =1 ;
#--------------------------------------------------------------------------------
# msfRd reads MSF files input format
# in: $fileInLoc
# out: ($Lok,$msg,$msfIn{}) with:
# out: $msfIn{"NROWS"} number of alignments
# out: $msfIn{"id", $it} name for $it
# out: $msfIn{"seq",$it} sequence for $it
# err: ok-> 1,ok | error -> 0,message
#-------------------------------------------------------------------------------
$sbrName="lib-br:msfRd"; $fhinLoc="FHIN_"."msfRd";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
open("$fhinLoc","$fileInLoc") || do {
Carp::confess( "failed to open $fileInLoc: $!" );
return(0,"*** ERROR $sbrName: fileIn=$fileInLoc, not opened\n");
};
undef %msfIn; # ------------------------------
while (<$fhinLoc>) { # read file
chomp;
last if ($_ eq "//" ); # skip everything before ali sections
} undef %tmp;$ct=0;
while (<$fhinLoc>) { # read file
$_=~s/\n//g;
$_=~s/^\s*|\s*$//g; # purge leading blanks
$rd=$_;
$tmp=$_;
$tmp=~s/^\s*\d+[\s\t\.\,\d]+$//g;
next if (length($tmp)<1); # skip lines empty or with numbers, only
# --------------------
# from here on: 'id sequence'
$id= $rd; $id =~s/^\s*(\S+)\s*.*$/$1/;
$seq=$rd; $seq=~s/^\s*(\S+)\s+(\S.*)$/$2/;
$seq=~s/\s//g;
if (! defined $tmp{$id}){ # new
++$ct;$tmp{$id}=$ct;
$msfIn{"id",$ct}= $id;
$msfIn{"seq",$ct}=$seq;}
else {
$ptr=$tmp{$id};
$msfIn{"seq",$ptr}.=$seq;
}
}
close($fhinLoc);
$msfIn{"NROWS"}=$ct;
return(1,"ok $sbrName",%msfIn);
} # end of msfRd
#===============================================================================
sub msfShorten {
local($fileInLoc,$fileOutLoc) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# msfShorten shortens names to <= 15 characters
# in: $fileInLoc
# out: 1|0,msg, implicit:
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."msfShorten";
$fhinLoc="FHIN_"."msfShorten";$fhoutLoc="FHOUT_"."msfShorten";
# check arguments
return(&errSbr("not def fileInLoc!")) if (! defined $fileInLoc);
return(&errSbr("not def fileOutLoc!")) if (! defined $fileOutLoc);
return(&errSbr("no fileIn=$fileInLoc!")) if (! -e $fileInLoc);
# number of characters per line
$nperlineLoc=60;
# open MSF file
open($fhinLoc,$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(&errSbr("fileInLoc=$fileInLoc, not opened"));
$#tmp=0;
undef %msfIn; # ------------------------------
while (<$fhinLoc>) { # read file
$_=~s/\n//g;
push(@tmp,$_);
last if ($_ eq "//" ); # skip everything before ali sections
}
undef %tmp;$ct=0;
while (<$fhinLoc>) { # read file
$_=~s/\n//g;
$_=~s/^\s*|\s*$//g; # purge leading blanks
$rd=$_;
$tmp=$_;
$tmp=~s/^\s*\d+[\s\t\.\,\d]+$//g;
next if (length($tmp)<1); # skip lines empty or with numbers, only
# --------------------
# from here on: 'id sequence'
$id= $rd; $id =~s/^\s*(\S+)\s*.*$/$1/;
$seq=$rd; $seq=~s/^\s*(\S+)\s+(\S.*)$/$2/;
$seq=~s/\s//g;
if (! defined $tmp{$id}){ # new
++$ct;$tmp{$id}=$ct;
$msfIn{"id",$ct}= $id;
$msfIn{"seq",$ct}=$seq;}
else {
$ptr=$tmp{$id};
$msfIn{"seq",$ptr}.=$seq;
}
}
close($fhinLoc);
$msfIn{"NROWS"}=$ct;
# ------------------------------
# now shorten names
# ------------------------------
undef %msfIn2;
foreach $it (1..$msfIn{"NROWS"}){
if (length($msfIn{"id",$it})<=15) {
$msfIn2{$msfIn{"id",$it}}=1;
next;}
# too long
$id=$msfIn{"id",$it};
$id=~s/^.*\|//g; # purge paths
# purge blanks
$id=~s/\s//g if (length($id)>15);
# purge extensions
$id=~s/\.[a-z]//g if (length($id)>15);
# cleave
$id=substr($id,1,15) if (length($id)>15);
# not unique
if (defined $msfIn2{$id}){
$id=substr($id,1,12);
$ct=1;$idmsfIn=$id.$ct;
while(defined $msfIn2{$idmsfIn}){
++$ct;
last if ($ct>999);}
$id=$idmsfIn;}
return(0,"*** $sbrName: shoot id=$id, orig=",,", failed shortening\n")
if (defined $msfIn2{$id} || length($id)>15);
$msfIn2{$id}=1;
$msfIn{"id",$it}=$id;
}
undef %msfIn2;
# ------------------------------
# change header
$#tmp2=$ct=0;
foreach $tmp (@tmp){
if ($tmp !~/[Nn]ame\s*:\s*(\S+)/){
push(@tmp2,$tmp);}
else {
++$ct;
$tmp=~s/([Nn]ame\s*:\s*)\S+/$1$msfIn{"id",$ct}/;
push(@tmp2,$tmp);}}
@tmp=@tmp2; $#tmp2=0;
# ------------------------------
# write new MSF
# ------------------------------
$lenloc=length($msfIn{"seq",1});
open($fhoutLoc,">".$fileOutLoc) || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(&errSbr("fileOutLoc=$fileOutLoc, not created"));
# get longest name
$maxlen=0;
foreach $itprot (1..$msfIn{"NROWS"}){
$maxlen=length($msfIn{"id",$itprot}) if (length($msfIn{"id",$itprot}) > $maxlen);
}
$ctres=length($msfIn{"seq",1});
# header
foreach $tmp (@tmp){
$tmp=~s/$lenloc/$ctres/g; # replace old by new length
print $fhoutLoc $tmp,"\n";
}
# body
for($it=1;$it<=$ctres;$it+=$nperlineLoc){
print $fhoutLoc
"\n";
printf $fhoutLoc
"%-".$maxlen."s %-s\n",
" ",$it." " x ($nperlineLoc-length($it)-length($it+$nperlineLoc)) .($it+$nperlineLoc);
foreach $itprot (1..$msfIn{"NROWS"}){
printf $fhoutLoc
"%-".$maxlen."s %-s\n",
$msfIn{"id",$itprot},substr($msfIn{"seq",$itprot},$it,$nperlineLoc),"\n";
}
}
close($fhoutLoc);
return(0,"*** $sbrName: no output file=$fileOutLoc!")
if (! -e $fileOutLoc);
# clean up
undef %msfIn; undef %tmp; # slim-is-in
$#tmp=0;
return(1,"ok $sbrName");
} # end of msfShorten
#==============================================================================
sub msfWrt {
local($fhoutLoc,%input) = @_ ;
local(@nameLoc,@stringLoc,$tmp,$sbrName,$Lok);
$[ =1 ;
if( $par{debug} ){ cluck("msfWrt ".join(', ', map{"$_ => $input{$_}";}(keys(%input)))); }
#--------------------------------------------------------------------------------
# msfWrt writing an MSF formatted file of aligned strings
# in: $fileMsf,$input{}
# $input{"NROWS"} number of alignments
# $input{"FROM"} name of input file
# $input{"TO"} name of output file
# $input{$it} sequence identifier ($name)
# $input{SEQS}->{$name} sequence for $name
#--------------------------------------------------------------------------------
$sbrName="msfWrt";
if( $input{"NROWS"} && !$input{SEQS} ){ confess("no SEQS in %input - update calling code"); }
# ------------------------------
$#nameLoc=$#tmp=0; # process input
foreach $it (1..$input{"NROWS"}){
$name=$input{$it};
push(@nameLoc,$name); # store the names
push(@stringLoc,$input{SEQS}->{$name}); } # store sequences
$FROM=$input{"FROM"} if (defined $input{"FROM"});
$TO= $input{"TO"} if (defined $input{"TO"});
# ------------------------------
# write into file
print $fhoutLoc
"MSF of: ",$FROM," from: 1 to: ",length($stringLoc[1])," \n",
$TO," MSF: ",length($stringLoc[1]),
" Type: P Jul-11-1961 14:00 Check: 1933 ..\n \n \n";
foreach $it (1..$#stringLoc){
printf
$fhoutLoc "Name: %-20s Len: %-5d Check: 2222 Weight: 1.00\n",
$nameLoc[$it],length($stringLoc[$it]);
}
print $fhoutLoc " \n","\/\/\n"," \n";
for($it=1;$it<=length($stringLoc[1]);$it+=50){
foreach $it2 (1..$#stringLoc){
printf $fhoutLoc "%-20s",$nameLoc[$it2];
foreach $it3 (1..5){
last if (length($stringLoc[$it2])<($it+($it3-1)*10));
printf $fhoutLoc
" %-10s",substr($stringLoc[$it2],($it+($it3-1)*10),10);}
print $fhoutLoc "\n";}
print $fhoutLoc "\n"; }
print $fhoutLoc "\n";
close($fhoutLoc);
$#nameLoc=$#stringLoc=0; # save space
return(1);
} # end of msfWrt
#==============================================================================
sub open_file {
local ($file_handle,$file_name,$log_file) = @_ ;
local ($temp_name) ;
#-------------------------------------------------------------------------------
# open_file opens file, writes warning asf
#-------------------------------------------------------------------------------
$temp_name = $file_name ;
$temp_name =~ s/^>>|^>//g ;
if ( ($file_name =~ /^>>/ ) && ( ! -e $temp_name ) ) {
print
"*** INFO (open_file): append file=$temp_name, does not exist-> create it\n" ;
open ($file_handle, ">$temp_name") || Carp::confess( "failed to open $temp_name: $!" ) || ( do {
cluck "***\t Cannot create new file: $temp_name\n" ;
if ( $log_file ) {
print $log_file "***\t Cannot create new file: $temp_name\n" ;}
return (0);
} );
close ("$file_handle") ;}
open ($file_handle, "$file_name") || Carp::confess( "failed to open $file_name: $!" ) || ( do {
cluck "*** ERROR lib-br:open_file: Cannot open file '$file_name'\n" ;
if ( $log_file ) {
print $log_file "*** lib-br:open_file: Cannot create new file '$file_name'\n" ;}
return(0);
} );
return(1);
} # end of open_file
#===============================================================================
sub pdbExtrSequence {
local($fileInLoc,$chainInLoc,$LskipNucleic) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# pdbExtrSequence reads the sequence in a PDB file
# in: $fileInLoc= PDB file
# in: $chainInLoc= chains to read ('A,B,C' for many)
# ='*' to read all
# in: $LskipNucleic= skip if nucleic acids
# out: 1|0,msg,%pdb as implicit reference with:
# out: $pdb{"chains"}="A,B" -> all chains found ('none' for not specified)
# $pdb{$chain}= sequence for chain $chain
# (='none' for not specified chain)
# NOTE: 'X' used for hetero-atoms, or for symbol 'U'
# $pdb{"header"}
# $pdb{"compnd"}
# $pdb{"source"}
# $pdb{"percentage_strange"}=
# percentage (0-100) of 'strange' acids ('!X')
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."pdbExtrSequence";
$fhinLoc="FHIN_"."pdbExtrSequence";$fhoutLoc="FHOUT_"."pdbExtrSequence";
# check arguments
return(&errSbr("not def fileInLoc!")) if (! defined $fileInLoc);
return(&errSbr("not def chainInLoc!")) if (! defined $chainInLoc);
return(&errSbr("not def LskipNucleic!")) if (! defined $LskipNucleic);
$chainInLoc="*" if (length($chainInLoc) < 1 || $chainInLoc =~/\s/);
return(&errSbr("no fileIn=$fileInLoc!")) if (! -e $fileInLoc);
# open file
open($fhinLoc,$fileInLoc) || Carp::confess( "failed to open $fileInLoc: $!" ) || return(&errSbr("fileInLoc=$fileInLoc, not opened"));
undef %pdb; # security
$#chainLoc=0;
$ctLine=0; # count lines in file (for error)
$ctStrange=0; # count amino acids (non ACGT)
$ctRes=0;
$Lflag=0; # set to 1 as soon as sequence found
# ------------------------------
while (<$fhinLoc>) { # read file
# ------------------------------
++$ctLine;
# skip anything before sequence
if ($_!~/^SEQRES/) {
#HEADER HYDROLASE (SERINE PROTEINASE) 24-APR-89 1P06 1P06 3
if ($_=~/^HEADER\s+(.*)\d\d\-[A-Z][A-Z][A-Z]\-\d\d\s*\d\w\w\w\s+/){
$pdb{"header"}=$1;
$pdb{"header"}=~s/^\s*|\s*$//g;
$pdb{"header"}=~s/^\s\s+|\s//g;
next; }
#COMPND ALPHA-LYTIC PROTEASE (E.C.3.4.21.12) COMPLEX WITH 1P06 4
#COMPND 2 METHOXYSUCCINYL-*ALA-*ALA-*PRO-*PHENYLALANINE BORONIC ACID 1P06 5
if ($_=~/^COMPND\s+(.*)\s+\d\w\w\w\s+\d+\s*$/) {
$pdb{"compnd"}="" if (! defined $pdb{"compnd"});
$pdb{"compnd"}.=$1;
$pdb{"compnd"}=~s/^\s*|\s*$//g;
$pdb{"compnd"}=~s/\s\s+/ /g; # purge many blanks
next; }
#SOURCE (LYSOBACTER $ENZYMOGENES 495) 1P06 6
if ($_=~/^SOURCE\s+(.*)\s+\d\w\w\w\s+\d+\s*$/) {
$pdb{"source"}=$1; $pdb{"source"}=~s/[\(\)\$]//g;
$pdb{"source"}=~s/^\s*|\s*$//g;
$pdb{"source"}=~s/\s\s+/ /g; # purge many blanks
next; }
last if ($Lflag); # end after read
next; }
# delete stuff at ends
#....,....1....,....2....,....3....,....4....,....5....,....6....,....7....,....8
#SEQRES 1 A 198 ALA ASN ILE VAL GLY GLY ILE GLU TYR SER ILE ASN ASN 1P06 74
$Lflag=1; # sequence found
$_=~s/\n//g;
$line=substr($_,11);
$line=substr($line,1,60);
$chainRd=$line; $chainRd=~s/^\s*(\D*)\d+.*$/$1/g; $chainRd=~s/\s//g;
$chainRd="*" if (! defined $chainRd || length($chainRd)<1);
# skip if wrong chain
next if ($chainInLoc ne "*" && $chainRd ne $chainInLoc);
# rename chain for non-specified
$chainRd="none" if ($chainRd eq "*");
# get sequence part
$seqRd3= $line; $seqRd3=~s/^\D*\d+(\D+).*$/$1/g;
$seqRd3=~s/^\s*|\s*$//g; # purge trailing spaces
# strange
next if (! defined $seqRd3 || length($seqRd3)<3);
# split into array of 3-letter residues
@tmp=split(/\s+/,$seqRd3);
# ------------------------------
# end if is nucleic that was NOT
# wanted!
return(2,"nucleic","")
if ($LskipNucleic && $tmp[1]=~/^[ACGT]$/);
# <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
$seqRd1=""; # 3 letter to 1 letter
foreach $tmp (@tmp) {
($Lok,$msg,$oneletter)=&amino_acid_convert_3_to_1($tmp);
# HETERO atom?
if (! $Lok && $oneletter eq "unk") {
print "-*- WARN $fileInLoc ($ctLine) residue =$tmp\n";
$oneletter="X";}
elsif (! $Lok || $oneletter !~/^[A-Z]$/) {
$msgErr="*** $sbrName ($fileInLoc): line=$ctLine, problem with conversion to 1 letter:\n";
return(0,$msgErr.$msg); }
$seqRd1.=$oneletter; }
# first
if (! defined $pdb{$chainRd}) {
push(@chainLoc,$chainRd);
$pdb{$chainRd}=""; }
# append to current chain
$pdb{$chainRd}.=$seqRd1;
# count non ACGT
@tmp=split(//,$seqRd1);
$ctRes+=$#tmp; # count residues
foreach $tmp (@tmp) {
next if ($tmp!~/^[A-Z]$/); # exclude strange stuff
++$ctStrange;}
} close($fhinLoc);
$pdb{"chains"}=join(',',@chainLoc);
$pdb{"percentage_strange"}=0;
$pdb{"percentage_strange"}=100*int($ctStrange/$ctRes) if ($ctStrange && $ctRes);
return(1,"ok $sbrName",\%pdb);
} # end of pdbExtrSequence
#==============================================================================
sub pirRdMul {
local($fileInLoc,$extr) = @_ ;
local($sbrName,$fhinLoc,$msg,$Lok,$seq,$id);
$[ =1 ;
#-------------------------------------------------------------------------------
# pirRdMul reads the sequence from a PIR file
# in: file,$extr with:
# $extr = '1,5,6', i.e. list of numbers to read
# out: 1|0,$id,$seq (note: many ids/seq separated by '\n'
# err: ok=(1,'ok'), err=(0,'msg')
#-------------------------------------------------------------------------------
$sbrName="lib-br:pirRdMul";$fhinLoc="FHIN_"."$sbrName";
open("$fhinLoc","$fileInLoc") || Carp::confess( "failed to open $fileInLoc: $!" ) ||
return(0,"*** ERROR $sbrName: fileIn=$fileInLoc not opened\n");
$extr=~s/\s//g if (defined $extr);
$extr=0 if (! defined $extr || $extr =~ /[^0-9\,]/);
if ($extr){@tmp=split(/,/,$extr); undef %tmp;
foreach $tmp(@tmp){
$tmp{$tmp}=1;}}
$ct=$ctRd=$ctProt=0; # ------------------------------
while (<$fhinLoc>) { # read the file
$_=~s/\n//g;
if ($_ =~ /^\s*>/){ # (1) = id (>P1;)
$Lread=0;
++$ctProt;
$id=$_;$id=~s/^\s*>\s*P1?\s*\;\s*//g;$id=~s/(\S+)[\s\n]*.*$/$1/g;$id=~s/^\s*|\s*$//g;
$id.="_";
$id.=<$fhinLoc>; # (2) still id in second line
$id=~s/[\s\t]+/ /g;
$id=~s/_\s*$/g/;
$id=~s/^[\s\t]*|[\s\t]*$//g;
if (! $extr || ($extr && defined $tmp{$ctProt} && $tmp{$ctProt})){
++$ctRd;$Lread=1;
$tmp{"$ctRd","id"}=$id;
$tmp{"$ctRd","seq"}="";}}
elsif($Lread){ # (3+) sequence
$_=~s/[\s\*]//g;
$tmp{"$ctRd","seq"}.="$_";}}close($fhinLoc);
# ------------------------------
$seq=$id=""; # join to long strings
if ($ctRd > 1) {
foreach $it(1..$ctRd){
$id.= $tmp{$it,"id"}."\n";
$tmp{$it,"seq"}=~s/\s//g;$tmp{$it,"seq"}=~s/\*$//g;
$seq.=$tmp{$it,"seq"}."\n";} }
else { $it=1;
$id= $tmp{$it,"id"};
$tmp{$it,"seq"}=~s/\s//g;$tmp{$it,"seq"}=~s/\*$//g;
$seq=$tmp{$it,"seq"}; }
$#tmp=0;undef %tmp; # save memory
return(0,"*** ERROR $sbrName: file=$fileInLoc, nali=$ct, wanted: (rd=$rd)\n"," ")
if (length($seq)<1);
return(1,$id,$seq);
} # end of pirRdMul
#==============================================================================
sub pirWrtMul {
local($fileOutLoc,%tmp) = @_ ;
local($sbrName,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# pirWrtMul writes a list of sequences in PIR format
# in: $fileOut,$tmp{} with:
# in: $tmp{"NROWS"} number of sequences
# in: $tmp{"id",$ct} id for sequence $ct
# in: $tmp{"seq",$ct} seq for sequence $ct
# out: file
# err: err -> 0,message
# err: ok -> 1,ok
# err: warn -> 2,not enough written
#-------------------------------------------------------------------------------
$sbrName="lib-br:pirWrtMul";$fhoutLoc="FHOUT_"."$sbrName";
return(0,"*** ERROR $sbrName: no tmp{NROWS} defined\n") if (! defined $tmp{"NROWS"});
open("$fhoutLoc",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(0,"*** ERROR $sbrName: '$fileOutLoc' not opened for write\n");
$ctOk=0;
foreach $itpair (1..$tmp{"NROWS"}){
next if (! defined $tmp{"id",$itpair} || ! defined $tmp{"seq",$itpair});
++$ctOk;
# some massage
$tmp{"id",$itpair}=~s/[\s\t\n]+/ /g;
$tmp{"seq",$itpair}=~s/[\s\t\n]+//g;
# write
print $fhoutLoc ">P1\; ",$tmp{"id",$itpair},"\n";
print $fhoutLoc $tmp{"id",$itpair},"\n";
$tmp{"seq",$itpair}.="*";
$lenHere=length($tmp{"seq",$itpair});
for($it=1; $it<=$lenHere; $it+=50){
$tmpWrt= "";
foreach $it2 (0..4){
$itHere=($it + 10*$it2);
last if ( $itHere >= $lenHere);
$nchunk=10;
$nchunk=1+($lenHere-$itHere) if ( (10 + $itHere) > $lenHere);
$tmpWrt.= sprintf(" %-10s",substr($tmp{"seq",$itpair},$itHere,$nchunk));
}
print $fhoutLoc $tmpWrt,"\n";
}
}
close($fhoutLoc);
return(0,"*** ERROR $sbrName: no sequence written\n")
if (! $ctOk);
return(2,"-*- WARN $sbrName: wrote fewere sequences than expected\n")
if ($ctOk!=$tmp{"NROWS"});
return(1,"ok $sbrName");
} # end of pirWrtMul
#===============================================================================
sub pirWrtOne {
local($fileOutLoc,$idLoc,$seqLoc) = @_ ;
local($sbrName,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# pirWrtOne writes one sequence in PIR format
# in: $fileOut,$id,$seq,
# out: file
# err: err -> 0,message
# err: ok -> 1,ok
#-------------------------------------------------------------------------------
$sbrName="lib-br:pirWrtOne";$fhoutLoc="FHOUT_"."$sbrName";
return(0,"*** ERROR $sbrName: no seq defined\n") if (! defined $seqLoc);
open("$fhoutLoc",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(0,"*** ERROR $sbrName: '$fileOutLoc' not opened for write\n");
# some massage
$idLoc=~s/[\s\t\n]+/ /g;
$seqLoc=~s/[\s\t\n]+//g;
# write
print $fhoutLoc ">P1\; ",$idLoc,"\n";
print $fhoutLoc $idLoc,"\n";
$seqLoc.="*"; # add star
$lenHere=length($seqLoc);
for($it=1; $it<=$lenHere; $it+=50){
$tmpWrt= "";
foreach $it2 (0..4){
$itHere=($it + 10*$it2);
last if ( $itHere >= $lenHere);
$nchunk=10;
$nchunk=1+($lenHere-$itHere) if ( (10 + $itHere) > $lenHere);
$tmpWrt.= sprintf(" %-10s",substr($seqLoc,$itHere,$nchunk));
}
print $fhoutLoc $tmpWrt,"\n";
}
close($fhoutLoc);
return(0,"*** ERROR $sbrName: no sequence written\n")
if (! -e $fileOutLoc);
return(1,"ok $sbrName");
} # end of pirWrtOne
#===============================================================================
sub rdRdbAssociative {
local ($fileInLoc,@des_in) = @_ ;
local ($sbr_name,$fhinLoc,$Lhead,$Lbody,$Lfound,$it,$itrd,@tmp,$tmp,$des_in,$rd,
@des_head,@des_headin,@des_bodyin,@des_body,%ptr_rd2des,$nrow_rd,%rdrdb,
$Lscreen);
$[ =1 ;
#--------------------------------------------------------------------------------
# rdRdbAssociative reads content of an RDB file into associative array
# in: Names used for columns in perl file, e.g.,
# "header,NALIGN,body,POS,NPROT" as arguments passed
# would result in:
# reading anything in file header using the keyword 'NALIGN'
# reading the columns named POS and NPROT
# out: rdrdb{"NALIGN"},rdrdb{"POS","ct"},rdrdb{"NPROT","ct"},
# where ct counts the rows read,
# rdrdb{"NROWS"} returns the numbers of rows read
#--------------------------------------------------------------------------------
# avoid warning
$READHEADER="";
$Lscreen=1;
# set some defaults
$fhinLoc="FHIN_RDB";$sbr_name="rdRdbAssociative";
# get input
$Lhead=$Lbody=$#des_headin=$#des_bodyin=0;
foreach $des_in (@des_in){
if ($des_in=~/^not_screen/) {$Lscreen=0;}
elsif((!$Lhead) && ($des_in=~/head/)){$Lhead=1;$Lhead_all=1;}
elsif((!$Lbody) && ($des_in=~/body/)){$Lbody=1;$Lhead=0; }
elsif($Lhead) {push(@des_headin,$des_in);}
elsif($Lbody) {$des_in=~s/\n|\s//g;;
push(@des_bodyin,$des_in);}
else {
print "*** WARNING $sbr_name: input '$des_in' not recognised.\n";} }
if ($Lscreen) { print "--- $sbr_name: header \t ";
foreach $it (@des_headin){print"$it,";}print"\n";
print "--- $sbr_name: body \t ";
foreach $it (@des_bodyin){print"$it,";}print"\n"; }
# --------------------------------------------------
# read RDB file
# --------------------------------------------------
open("$fhinLoc","$fileInLoc") || Carp::confess( "failed to open $fileInLoc: $!" );
# out: $READHEADER :whole header, one string
# @READCOL : all columns
# @READNAME :names of columns
&rdRdbAssociativeNum($fhinLoc,0);
close($fhinLoc);
# ------------------------------
$#des_head=0; # process header
@tmp=split(/\#\s?/,$READHEADER);
if ($#des_headin>=1){
foreach $des_in (@des_headin) {
$Lfound=0;
foreach $rd (@tmp){
if ($rd =~ /^(PARA\s*:?\s*)?$des_in\s*[ :,\;=]/){
$tmp=$rd;$tmp=~s/\n|\s$//g;$tmp=~s/^.*$des_in//g;$tmp=~s/^\s*//g;
$tmp=~s/^[\s:\t]*//g;
if (defined $rdrdb{"$des_in"}){
$rdrdb{"$des_in"}.="\t".$tmp;}
else {
$rdrdb{"$des_in"}=$tmp;}
push(@des_head,$des_in);$Lfound=1;} }
print
"--- $sbr_name: \t expected to find in header key word:\n",
"--- \t '$des_in', but not in file '$fileInLoc'\n"
if (!$Lfound && $Lscreen); }}
elsif ($Lhead_all) { # whole header into $rdrdb{"header"}
$rdrdb{"header"}="";
foreach $rd (@tmp) { $rd=~s/^\s?|\n//g;
$rdrdb{"header"}.="# ".$rd."\n"; }}
# ------------------------------
$#des_body=0; # get column numbers to be read
foreach $des_in (@des_bodyin) {
$Lfound=0;
for($it=1; $it<=$#READNAME; ++$it) {
$rd=$READNAME[$it];$rd=~s/\s//g;
if ($rd eq $des_in) {
$ptr_rd2des{"$des_in"}=$it;push(@des_body,$des_in);$Lfound=1;
last;} }
if((!$Lfound) && $Lscreen){
print"--- $sbr_name: \t expected to find column name:\n";
print"--- \t '$des_in', but not in file '$fileInLoc'\n";}}
# ------------------------------
# get format
foreach $des_in(@des_bodyin) {
$it=$ptr_rd2des{"$des_in"};
if ( defined $it && defined $READFORMAT[$it] ) {
$rdrdb{"$des_in","format"}=$READFORMAT[$it];}
else {
$rdrdb{"$des_in","format"}="8";}}
$nrow_rd=0;
foreach $des_in(@des_body) {
$itrd=$ptr_rd2des{"$des_in"};
@tmp=split(/\t/,$READCOL[$itrd]);
if ($nrow_rd==0) {$nrow_rd=$#tmp;}
elsif($nrow_rd!=$#tmp){print "*** WARNING $sbr_name: different number of rows\n";
print "*** in RDB file '$fileInLoc' for rows with ".
"key=$des_in, column=$itrd, prev=$nrow_rd, now=$#tmp,\n";}
for ($it=1; $it<=$#tmp; ++$it){
$rdrdb{"$des_in",$it}=$tmp[$it];
$rdrdb{"$des_in",$it}=~s/\s//g;}
}
$rdrdb{"NROWS"}=$rdrdb{"NROWS"}=$nrow_rd;
# ------------------------------
# safe memory
$READHEADER=""; $#READCOL=$#READNAME=$#READFORMAT=0;
$#des_headin=$#des_body=$#tmp=$#des_head=0;
undef %ptr_rd2des;
$#des_in=0; # slim_is_in !
return (%rdrdb);
} # end of rdRdbAssociative
#===============================================================================
sub rdRdbAssociativeNum {
local ($fhLoc2,@readnum) = @_ ;
local ($ctLoc, @tmpar, $it, $ipos, $tmp);
$[ =1 ;
#----------------------------------------------------------------------
# rdRdbAssociativeNum reads from a file of Michael RDB format:
# in: $fhLoc,@readnum,$readheader,@readcol,@readname,@readformat
# $fhLoc: file handle for reading
# @readnum: vector containing the number of columns to be read, if empty,
# then all columns will be read!
# $READHEADER: returns the complete header as one string
# @READCOL: returns all columns to be read (tab separated)
# @READNAME: returns the names of the columns
# @READFORMAT: returns the format of each column
#----------------------------------------------------------------------
$READHEADER=""; $#READCOL=$#READNAME=$#READFORMAT=0;
for ($it=1; $it<=$#readnum; ++$it) { $READCOL[$it]=""; }
$ctLoc= 0;
$tmpct=0;
while ( <$fhLoc2> ) { # ------------------------------
++$tmpct; # header
if ( /^\#/ ) {
$READHEADER.= "$_";
next; }
$rd=$_;$rd=~s/^\s+|\s+$//g;
next if (length($rd)<2);
++$ctLoc; # count non-comment
# ------------------------------
# names
if ($ctLoc==1){
$rd=$_;$rd=~s/^\t+|\t$//g;@tmpar=split(/\t/,$rd);
# process wild card
if ($#readnum==0 || $readnum[1]==0 ||
$readnum[1] !~ /[0-9]/ || ! defined $readnum[1] ) {
foreach $it (1..$#tmpar){
$readnum[$it]=$it;
$READCOL[$it]=""; }}
foreach $it (1..$#readnum){
$tmp_name=$tmpar[$readnum[$it]];$tmp_name=~s/\s|\n//g;
$READNAME[$it]="$tmp_name"; }
next; }
# ------------------------------
# skip format?
if ($ctLoc==2 && $rd!~/\d+[SNF]\t|\t\d+[SNF]/){
++$ctLoc; }
if ($ctLoc==2) { # read format
$rd=$_;$rd=~s/^\t+|\t$//g;@tmpar=split(/\t/,$rd);
foreach $it (1..$#readnum){
$ipos=$readnum[$it];$tmp=$tmpar[$ipos]; $tmp=~s/\s//g;
$READFORMAT[$it]=$tmp; }
next; }
# ------------------------------
# data
$rd=$_;$rd=~s/^\t+|\t$//g;@tmpar=split(/\t/,$rd);
foreach $it (1..$#readnum){
next if (! defined $tmpar[$readnum[$it]]);
$READCOL[$it].=$tmpar[$readnum[$it]] . "\t"; }
}
# ------------------------------
# massage FORMAT/COL/NAME
foreach $it (1..$#READCOL){
$READFORMAT[$it]=~ s/^\s+//g if (defined $READFORMAT[$it]);
$READFORMAT[$it]=~ s/\t$|\n//g if (defined $READFORMAT[$it]);
$READNAME[$it]=~ s/^\s+//g if ($#READNAME>0);
$READNAME[$it]=~s/\t|\n//g;
$READNAME[$it]=~s/\n//g if ($#READNAME>0);
$READCOL[$it] =~ s/\t$|\n//g; # correction: last not return!
}
} # end of rdRdbAssociativeNum
#===============================================================================
sub safCompress {
local($fileInLoc,$fileOutLoc) = @_ ;
local($sbrName,$fhinLoc,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# safCompress deletes insertions in guide sequence
# in: $fileInLoc
# out: 1|0,msg, implicit:
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName=$tmp."safCompress";
$fhinLoc="FHIN_"."safCompress";$fhoutLoc="FHOUT_"."safCompress";
# check arguments
return(&errSbr("not def fileInLoc!")) if (! defined $fileInLoc);
return(&errSbr("not def fileOutLoc!")) if (! defined $fileOutLoc);
return(&errSbr("no fileIn=$fileInLoc!")) if (! -e $fileInLoc);
# number of characters per line
$nperlineLoc=60;
($Lok,$msg,%safIn)=
&safRd($fileInLoc); return(&errSbrMsg("safRd failed on fileInLoc=$fileInLoc!",
$msg)) if (! $Lok);
# ------------------------------
# now compress insertions in guide
# ------------------------------
$ctcleave=$ctres=0;
$lenloc=length($safIn{"seq",1});
# all 0
foreach $itprot (1..$safIn{"NROWS"}){
$safIn{"new",$itprot}="";
}
# loop over all residues
foreach $itres (1..$lenloc){
# is residue
if (substr($safIn{"seq",1},$itres,1)=~/^[A-Za-z]/){
foreach $itprot (1..$safIn{"NROWS"}){
$safIn{"new",$itprot}.=substr($safIn{"seq",$itprot},$itres,1);
}
++$ctres;
next;}
# seems insertion
++$ctcleave;
}
# check: sum ok?
return(0,"*** $sbrName: failed at compressing ncleave=$ctcleave, nresnew=$ctres,".
" before=".$lenloc." file=$fileInLoc!")
if ($lenloc != ($ctcleave + $ctres));
# replace by cleaved version
foreach $itprot (1..$safIn{"NROWS"}){
$safIn{"seq",$itprot}=$safIn{"new",$itprot};
}
# ------------------------------
# write new SAF
# ------------------------------
open($fhoutLoc,">".$fileOutLoc) || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(&errSbr("fileOutLoc=$fileOutLoc, not created"));
# get longest name
$maxlen=0;
foreach $itprot (1..$safIn{"NROWS"}){
$maxlen=length($safIn{$itprot}) if (length($safIn{$itprot}) > $maxlen);
}
# body
for($it=1;$it<=$ctres;$it+=$nperlineLoc){
print $fhoutLoc
"\n";
printf $fhoutLoc
"%-".$maxlen."s %-s\n",
" ",$it." " x ($nperlineLoc-length($it)-length($it+$nperlineLoc)) .($it+$nperlineLoc);
foreach $itprot (1..$safIn{"NROWS"}){
printf $fhoutLoc
"%-".$maxlen."s %-s\n",
$safIn{"id",$itprot},substr($safIn{"seq",$itprot},$it,$nperlineLoc),"\n";
}
}
close($fhoutLoc);
return(0,"*** $sbrName: no output file=$fileOutLoc!")
if (! -e $fileOutLoc);
# clean up
undef %safIn; undef %tmp; # slim-is-in
$#tmp=0;
return(1,"ok $sbrName");
} # end of safCompress
#==============================================================================
sub safRd {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# safRd reads SAF format
# in: $fileOutLoc,
# out: ($Lok,$msg,$tmp{}) with:
# out: $tmp{"NROWS"} number of alignments
# out: $tmp{"id", $it} name for $it
# out: $tmp{"seq",$it} sequence for $it
# err: ok-> 1,ok | error -> 0,message
#-------------------------------------------------------------------------------
$sbrName="lib-br:"."safRd";$fhinLoc="FHIN_"."safRd";
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
$LverbLoc=0;
open("$fhinLoc","$fileInLoc") || Carp::confess( "failed to open $fileInLoc: $!" ) ||
return(0,"*** ERROR $sbrName: fileIn=$fileInLoc, not opened\n");
$ctBlocks=$ctRd=$#nameLoc=0; undef %nameInBlock;
undef %tmp2;
undef %tmp; # --------------------------------------------------
# read file
while (<$fhinLoc>) { # --------------------------------------------------
$_=~s/\n//g;
next if ($_=~/^#/o); # ignore comments
last if ($_=~/^\s*[\-\_]+\s*$/); # stop when address
$line=$_;
# ignore lines with numbers, blanks, points only
$tmp=$_; $tmp=~s/[^A-Z]//gi;
next if (length($tmp)<1);
$line=~s/^\s*|\s*$//g; # purge leading blanks
# ------------------------------
# names
$nameRd=$line; $nameRd=~s/^(\S+)\s+.*$/$1/o;
# new name?
if (! defined $tmp2{"ptr",$nameRd}){
# maximal length: 14 characters (because of MSF2Hssp)
if (length($nameRd)<=14){
$nameTake=$nameRd;}
else {
$tmp=$nameRd;
#$tmp=~s/^.*\|//; # purge database
$tmp=~s/^[^|]*\|//o; # purge database
# make sure not too long
if(length($tmp)>14){
$tmp = substr($tmp,$[,14);
}
# make sure not too short
while (length($tmp)<2){
# nonsense name
$tmp .= substr( $nameRd, $[+length($tmp), 1 );
}
# security check
$Lok=0;
$Lok=1 if (length($tmp)>=2 &&
length($tmp)<=14);
if(! $Lok){ confess("could NOT find name '$tmp' for name=$nameRd"); }
$nameTake=$tmp;}
# make sure that it name unique
if (! defined $tmp2{$nameTake}){
$tmp2{$nameTake}=1;}
else {
$nameNew=$nameTmp=substr($nameTake,1,12);
$it=0;
while (defined $tmp2{$nameTmp} &&
$it<99){
++$it;
$nameTmp=$nameNew.$it; }
if (defined $tmp2{$nameTmp}){
$nameNew=$nameTmp=substr($nameRd,1,10);
$it=0;
while (defined $tmp2{$nameTmp} &&
$it<9999){
++$it;
$nameTmp=$nameNew.$it; }
}
else {
$tmp2{$nameTmp}=1; }
$nameTake=$nameTmp;
$tmp2{$nameTake}=1;}
# store a pointer
$tmp2{"ptr",$nameRd}=$nameTake;
}
else { # old name: translate
$nameTake=$tmp2{"ptr",$nameRd}; }
# ------------------------------
# sequences
$seq=$line;$seq=~s/^\s*//;$seq=~s/^[^\s\t]+//;$seq=~s/\s//g;
# next if ($seq =~/^ACDEFGHIKLMNPQRSTVWXYZ/i); # check this!!
print "--- $sbrName: nameRd=$nameRd, nameTake=$nameTake, seq=$seq,\n"
if ($LverbLoc);
# ------------------------------
# guide sequence: determine length
# NOTE: no 'left-outs' allowed here
# ------------------------------
$nameFirst=$nameTake if ($#nameLoc==0); # detect first name
if ($nameTake eq "$nameFirst"){
++$ctBlocks; # count blocks
undef %nameInBlock;
if ($ctBlocks == 1){
$lenFirstBeforeThis=0;}
else {
$lenFirstBeforeThis=length($tmp{"seq","1"});}
if ($ctBlocks>1) { # manage proteins that did not appear
$lenLoc=length($tmp{"seq","1"});
foreach $itTmp (1..$#nameLoc){
$tmp{"seq",$itTmp}.="." x ($lenLoc-length($tmp{"seq",$itTmp}));}
}}
# ------------------------------
# ignore 2nd occurence of same name
next if (defined $nameInBlock{$nameTake}); # avoid identical names
# ------------------------------
# new name
if (! defined ($tmp{$nameTake})){
push(@nameLoc,$nameTake); ++$ctRd;
$tmp{$nameTake}=$ctRd;
$tmp{"id","$ctRd"}=$nameTake;
print "--- $sbrName: new name=$nameTake,\n" if ($LverbLoc);
if ($ctBlocks>1){ # fill up with dots
print
"--- $sbrName: file up for $nameTake, with :$lenFirstBeforeThis\n"
if ($LverbLoc);
$tmp{"seq","$ctRd"}="." x $lenFirstBeforeThis;}
else{
$tmp{"seq","$ctRd"}="";}}
# ------------------------------
# finally store
$seq=~s/[^A-Za-z]/\./g; # any non-character to dot
$seq=~tr/[a-z]/[A-Z]/;
$ptr=$tmp{$nameTake};
$tmp{"seq",$ptr}.=$seq;
$nameInBlock{$nameTake}=1; # avoid identical names
} close($fhinLoc);
# ------------------------------
# fill up ends
$lenLoc=length($tmp{"seq","1"});
foreach $itTmp (1..$#nameLoc){
$tmp{"seq",$itTmp}.="." x ($lenLoc-length($tmp{"seq",$itTmp}));}
$tmp{"NROWS"}=$ctRd;
$tmp{"names"}=join (',',@nameLoc); $tmp{"names"}=~s/^,*|,*$//;
$#nameLoc=0; undef %nameInBlock;
return(1,"ok $sbrName",%tmp);
} # end of safRd
#==============================================================================
sub safWrt {
local($fileOutLoc,%tmp) = @_ ;
local(@nameLoc,@stringLoc,$tmp,$sbrName,$Lok);
$[ =1 ;
#--------------------------------------------------------------------------------
# safWrt writing an SAF formatted file of aligned strings
# in: $fileOutLoc output file
# = "STDOUT" -> write to screen
# in: $tmp{"NROWS"} number of alignments
# in: $tmp{"id", $it} name for $it
# in: $tmp{"seq",$it} sequence for $it
# in: $tmp{"PER_LINE"} number of res per line (def=50)
# in: $tmp{"HEADER"} 'line1\n,line2\n'..
# with line1= '# NOTATION ..'
# out: 1|0,msg implicit: file
# err: ok-> 1,ok | error -> 0,message
#--------------------------------------------------------------------------------
$sbrName="lib-br:safWrt"; $fhoutLoc="FHOUT_safWrt";
# check input
return(0,"*** ERROR $sbrName: no acceptable output file ($fileOutLoc) defined\n")
if (! defined $fileOutLoc || length($fileOutLoc)<1 || $fileOutLoc !~/\w/);
return(0,"*** ERROR $sbrName: no input given (or not input{NROWS})\n")
if (! %tmp || ! defined $tmp{"NROWS"} );
return(0,"*** ERROR $sbrName: tmp{NROWS} < 1\n")
if ($tmp{"NROWS"} < 1);
$tmp{"PER_LINE"}=50 if (! defined $tmp{"PER_LINE"});
$fhoutLoc="STDOUT" if ($fileOutLoc eq "STDOUT");
# ------------------------------
# open new file
if ($fhoutLoc ne "STDOUT") {
open("$fhoutLoc",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(0,"*** ERROR $sbrName: failed opening fileOut=$fileOutLoc\n"); }
# ------------------------------
# write header
# ------------------------------
print $fhoutLoc "# SAF (Simple Alignment Format)\n","\# \n";
print $fhoutLoc $tmp{"HEADER"} if (defined $tmp{"HEADER"});
# get longest name
$maxlen=0;
foreach $itprot (1..$tmp{"NROWS"}){
$maxlen=length($tmp{"id",$itprot}) if (length($tmp{"id",$itprot}) > $maxlen);
}
# ------------------------------
# write data into file
# ------------------------------
for($itres=1; $itres<=length($tmp{"seq","1"}); $itres+=$tmp{"PER_LINE"}){
foreach $itpair (1..$tmp{"NROWS"}){
printf $fhoutLoc "%-".$maxlen."s ",$tmp{"id",$itpair};
# chunks of $tmp{"PER_LINE"}
$chunkEnd=$itres + ($tmp{"PER_LINE"} - 1);
foreach $itchunk ($itres .. $chunkEnd){
last if (length($tmp{"seq",$itpair}) < $itchunk);
print $fhoutLoc substr($tmp{"seq",$itpair},$itchunk,1);
# add blank every 10
print $fhoutLoc " "
if ($itchunk != $itres && (int($itchunk/10)==($itchunk/10)));
}
print $fhoutLoc "\n"; }
print $fhoutLoc "\n"; }
print $fhoutLoc "\n";
close($fhoutLoc);
$#nameLoc=$#stringLoc=0; # save space
return(0,"*** ERROR $sbrName: failed to write file $fileOutLoc\n") if (! -e $fileOutLoc);
return(1,"ok $sbrName");
} # end of safWrt
#==============================================================================
sub seqGenWrt {
local($seqInLoc,$idInLoc,$formOutLoc,$fileOutLoc,$fhErrSbr) = @_ ;
local($sbrName,$fhoutLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# seqGenWrt writes protein sequence in various output formats
# in: $seq,$id,$formOut,$fileOut,$fhErrSbr
# out: implicit: fileOut
# err: (1,'ok'), (0,'message')
#-------------------------------------------------------------------------------
$tmp=$0;$tmp=~s/^.*\/|\.pl//g;$tmp.=":";
$sbrName="lib-br:"."seqGenWrt"; $fhoutLoc="FHOUT_"."seqGenWrt";
# check arguments
return(0,"*** $sbrName: not def seqInLoc!") if (! defined $seqInLoc);
return(0,"*** $sbrName: not def idInLoc!") if (! defined $idInLoc);
return(0,"*** $sbrName: not def formOutLoc!") if (! defined $formOutLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
$fhErrSbr="STDOUT" if (! defined $fhErrSbr);
return(0,"*** $sbrName: sequence missing") if (length($seqInLoc)<1);
undef %tmp;
# ------------------------------
$tmp{"seq","1"}=$seqInLoc; # intermediate variable for seq
$tmp{"NROWS"}= 1;
$tmp{"id","1"}= $idInLoc;
$Lok=0;
# ------------------------------
# write output
if ($formOutLoc =~ /^fasta/){ ($Lok,$msg)=&fastaWrtMul($fileOutLoc,%tmp);}
elsif ($formOutLoc =~ /^pir/) { ($Lok,$msg)=&pirWrtMul($fileOutLoc,%tmp);}
elsif ($formOutLoc eq "saf") { ($Lok,$msg)=&safWrt($fileOutLoc,%tmp);}
elsif ($formOutLoc eq "msf") { $tmp{"FROM"}="unk";$tmp{"TO"}=$fileOutLoc;
$tmp{"1"}=$idInLoc;$tmp{SEQS}->{$idInLoc}=$seqInLoc;
open("$fhoutLoc",">$fileOutLoc") || Carp::confess( "failed to open $fileOutLoc: $!" ) ||
return(&errSbr("failed creating $fileOutLoc"));
$Lok=
&msfWrt($fhoutLoc,%tmp);
close($fhoutLoc);
return(&errSbr("failed writing msf=$fileOutLoc (msfWrt)"))
if (! $Lok);}
else {
return(0,"*** ERROR $sbrName output format $formOutLoc not supported\n");}
return(0,"*** ERROR $sbrName: failed to write $formOutLoc into $fileOutLoc\n")
if (! $Lok || ! -e $fileOutLoc);
return(1,"ok $sbrName");
} # end of seqGenWrt
#==============================================================================
sub swissRdSeq {
local($fileInLoc) = @_ ;
local($sbrName,$fhinLoc,$msg,$Lok,$seq,$id);
$[ =1 ;
#-------------------------------------------------------------------------------
# swissRdSeq reads the sequence from a SWISS-PROT file
# in: file
# out: (1,name,sequence in one string)
#-------------------------------------------------------------------------------
$sbrName="swissRdSeq";$fhinLoc="FHIN"."$sbrName";
$Lok= open("$fhinLoc","$fileInLoc") || Carp::confess( "failed to open $fileInLoc: $!" );
if (! $Lok){$msg="*** ERROR $sbrName: '$fileInLoc' not opened\n";
return(0,$msg,"error");}
$seq="";
while (<$fhinLoc>) {$_=~s/\n//g;
if ($_=~/^ID\s+(\S*)\s*.*$/){
$id=$1;}
last if ($_=~/^\/\//);
next if ($_=~/^[A-Z]/);
$seq.="$_";}close($fhinLoc);
$seq=~s/\s//g;
return(1,$id,$seq);
} # end of swissRdSeq
#==============================================================================
sub sysDate {
# local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# sysDate returns $Date
# out: $Date (May 30, 1998 59:39:03)
#-------------------------------------------------------------------------------
@tmp=("/home/rost/perl/ctime.pl","/home/rost/pub/perl/ctime.pl");
# ------------------------------
# get function
if (defined &localtime) {
foreach $tmp(@tmp){
if (-e $tmp){$Lok=require("$tmp");
last;}}
if (defined &ctime && &ctime && defined &localtime && &localtime){
# $date is e.g.: Oct:14:13:06:47:1993
# @Date is e.g.: Oct1413:06:471993
# &ctime(time) is e.g.: Thu Oct 14 13:06:47 1993
# print "xx enter\n";
@Date = split(' ',&ctime(time)) ; shift (@Date) ;
$Date="$Date[2] $Date[3], $Date[$#Date] $Date[4]";
return($Date);}
}
# ------------------------------
# or get system time
$localtime=`date`;
@Date=split(/\s+/,$localtime);
$Date="$Date[2] $Date[3], $Date[$#Date] $Date[4]";
return($Date);
} # end of sysDate
#===============================================================================
sub sysGetUserLoc {
$[ =1 ;
#-------------------------------------------------------------------------------
# sysGetUserLoc returns $USER (i.e. user name)
# out: USER
#-------------------------------------------------------------------------------
$sbrName="lib-ut:"."sysGetUserLoc";
if (defined $ENV{'USER'}){
return($ENV{'USER'});
}
$tmp=`whoami`;
return($tmp) if (defined $tmp && length($tmp)>0);
$tmp=`who am i`; # SUNMP
return($tmp) if (defined $tmp && length($tmp)>0);
return(0);
} # end of sysGetUserLoc
#==============================================================================
sub sysRunProg {
local ($cmd,$fileScrLoc,$fhErrLoc) = @_ ;
$[ =1;
#-------------------------------------------------------------------------------
# sysRunProg pipes arguments into $prog, and cats the output
# from $prog into a file
# in: $cmd,$fileScrLoc,$fhError
# in: $cmd='prog,arg1,arg2'
# in: where prog is the program, e.g. 'wc -l, file1,file2'
# in: $fileScrLoc is the output file
# in: NOTE: if not defined: buffered to STDOUT
# in: = 0 to surpress writing
# in: $fhError filehandle for ERROR writing
# NOTE: to STDOUT if not defined
# in: = 0 to surpress writing
# out: 0|1,message
# err: ok -> 1,ok | err -> 0,message
#-------------------------------------------------------------------------------
$sbrName="lib-sys:".( $par{"debug"} ? __FILE__.":".__LINE__ : '' ).":sysRunProg";
return(0,"*** ERROR $sbrName: argument program ($cmd) not defined\n")
if (! defined $cmd || length($cmd)<1);
$fhErrLoc=0 if (! defined $fhErrLoc);
$fileScrLoc=0 if (! defined $fileScrLoc);
# ------------------------------
# dissect arguments
($prog,@arg)=split(/,/o,$cmd);
if ($fhErrLoc && ! @arg) {
print $fhErrLoc "-*- WARN $sbrName: no arguments to pipe into:\n$prog\n";
}
elsif ($fhErrLoc && $par{debug}) {
print $fhErrLoc
"--- $sbrName: system cmd=\n$prog\n--- $sbrName: fileOut=$fileScrLoc cmd IN:\n$cmd\n"; }
# ------------------------------
# pipe output into file?
$Lpipe=0;
$Lpipe=1 if ($fileScrLoc);
$Lpipe=0 if ($prog =~ /\s+>>?\s+\S+\s*$/);
$prog.=" >> $fileScrLoc " if ($Lpipe);
# print "$cmd\n";exit;
# ------------------------------
# opens cmdtmp into pipe
# cluck/longmess fails with some perl bug!!!
if( $par{"debug"} ) { cluck( "|$prog" ); }
open (CMD, "|$prog") ||
Carp::confess( "*** $sbrName cannot open program '|$prog': $!" );
# get input arguments (< arg)
foreach $tmp (@arg) {
$tmp=~s/\n|^\s*|\s*$//; # delete end of line, and leading blanks
print CMD "$tmp\n";
if( $par{"debug"} ) { warn("CMD: $tmp|"); }
}
if( !close(CMD) ){ confess( "cmd '|$prog' failed: ".( $? >> 8 ) ); } # upon closing: cmdtmp < @out_command executed
return(1,"ok $sbrName");
} # end of sysRunProg
#==============================================================================
# library collected (end) lll
#==============================================================================
#===============================================================================
sub cleanUp {
local($sbrName,$fhinLoc,@tmp);
$[ =1 ;
#-------------------------------------------------------------------------------
# cleanUp deletes intermediate files
#-------------------------------------------------------------------------------
if ($scrName){$tmp="$scrName".":";}else{$tmp="";} $sbrName="$tmp"."cleanUp";
if ($#kwdRm>0){ # remove intermediate files
foreach $kwd (@kwdRm){
next if (! defined $file{$kwd} || ! -e $file{$kwd});
print "--- $sbrName unlink '",$file{$kwd},"'\n" if ($Lverb2);
unlink($file{$kwd});}}
foreach $kwd ("fileOutTrace","fileOutScreen"){
next if (! defined $par{$kwd} || ! -e $par{$kwd});
print "--- $sbrName unlink '",$par{$kwd},"'\n" if ($Lverb2);
unlink($par{$kwd});}
} # end of cleanUp
#===============================================================================
sub convAliGen {
local($fileInLoc,$fileOutLoc,$formIn,$formOut,$extOutLoc,$exeConvSeq,$fileMatGcg,
$doCompress,$frag,$extrLoc,$fileScreenLoc,$dirWork,$fhSbr) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convAliGen general converter for SAF|MSF|FASTAmul -> HSSP,SAF,MSF,FASTAmul,PIRmul
# in: $fileInLoc,$fileOutLoc,$formIn,$formOut,$extOutLoc,$frag,$extrLoc,
# + $fileScreenLoc,$dirWork,$fhSbr
# in: $fileInLoc file.Ali, file.out, format_of_output_file
# in: $fileOutLoc output file with converted sequence(s)
# in: NOTE: if many appended to @fileOut
# in: $formOut output format (lower caps)
# in: $extOutLoc extension of expected output (fragments into _beg_end$extension)
# in: $exeConvSeq FORTRAN program convert_seq
# in: $fileMatGcg Maxhom_GCG.metric (for converting to HSSP)
# in: $doCompress for conversion into HSSP : delete insertions in MASTER?
# in: $frag fragments e.g. '1-5,10-100'
# in: $extrIn number of protein to extract
# in: $fileScreen output file for system commands
# in: $dirWork directory for temporary files
# in: $fhSbr ERRORs of convert_seq
# out: converted file
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convAliGen";$fhinLoc="FHIN"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formIn!") if (! defined $formIn);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def exeConvSeq!") if (! defined $exeConvSeq);
return(0,"*** $sbrName: not def fileMatGcg!") if (! defined $fileMatGcg);
return(0,"*** $sbrName: not def doCompress!") if (! defined $doCompress);
return(0,"*** $sbrName: not def frag!") if (! defined $frag);
return(0,"*** $sbrName: not def extrLoc!") if (! defined $extrLoc);
return(0,"*** $sbrName: not def fileScreenLoc!") if (! defined $fileScreenLoc);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
return(0,"*** $sbrName: miss in file '$fileMatGcg'!") if (! -e $fileMatGcg);
#return(0,"*** $sbrName: miss exe '$exeConvSeq'!") if (! -e $exeConvSeq && ! -l $exeConvSeq);
$msgErr="";
return(0,"*** $sbrName: input format $formIn not supported\n")
if ($formIn !~/pir|gcg|swiss|msf|saf|fasta/);
$fhSysRunProg=0;
$fhSysRunProg="STDOUT" if ($par{"verbose"} || $par{"debug"});
$fileScreenLoc=0 if ($par{"debug"});
$#beg=$#end=0; # ------------------------------
if ($frag){ # extract fragments?
@tmp=split(/,/,$frag);
$#beg=$#end=0;
foreach $frag(@tmp){ next if ($frag !~ /\-/);$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
next if ($beg =~/\D/ || $end =~ /\D/);
push(@beg,$beg);push(@end,$end);}}
# ------------------------------
$#kwdRmTmp=0; # temporary files
# --------------------------------------------------
if ($formOut eq "hssp"){ # HSSP output
if ($#beg>1){ warn( "-*- WARN $sbrName: for $formIn -> HSSP currently only one fragment at a time!!" x 2 );}
$shortNames=1; # for HSSP: names shorter than 15 characters!
# ------------------------------
# (1) convert all seq to FASTA
if ($formIn =~ /^pir/ || $formIn eq "gcg" || $formIn eq "swiss" ){
$kwd=$formIn."-".$formOut ;push(@kwdRmTmp,$kwd);
$fileOutSeqTmp=$file{$kwd}=$dirWork.$par{"titleTmp"}.".fasta_tmp";
$fragHere=0; $fragHere="$beg[1]-$end[1]" if ($#beg>0);
return(&errSbr("more than one fragment not supported for converting ".
"$formIn to $formOut")) if ($#beg>1);
($Lok,$msg)=
&convSeq2fastaPerl($fileInLoc,$fileOutSeqTmp,$formIn,$fragHere,$shortNames);
return(&errSbrMsg("failed converting seq ($formIn) to FASTA",$msg)) if (! $Lok);
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# change input format
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
$formIn="fasta";}
else {
$fileOutSeqTmp=$fileInLoc;}
# ------------------------------
# (2) convert all to MSF
if( $par{debug} ){ cluck("convert all to MSF"); }
if ($formIn eq "saf" || $formIn =~/^fasta/){
$kwd=$formIn."-".$formOut;push(@kwdRmTmp,$kwd);
$fileOutMsfTmp=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_tmp";
$fragHere=0; $fragHere="$beg[1]-$end[1]" if ($#beg>0);
if ($formIn eq "saf"){
($Lok,$msg)=
&convSaf2many($fileOutSeqTmp,$fileOutMsfTmp,"msf",
$fragHere,$extrLoc,$fhSbr,$doCompress,$shortNames);}
elsif ($formIn =~ /^fasta/){
($Lok,$msg)=
&convFastamul2many($fileOutSeqTmp,$fileOutMsfTmp,"msf",
$fragHere,$extrLoc,$fhSbr,$doCompress,$shortNames);}
return(0,"*** ERROR $sbrName: failed to write msf ($fileOutMsfTmp) from $fileInLoc, ".
"to seq=$fileOutSeqTmp, for extr=$extrLoc".
$msg."\n") if (! $Lok || ! -e $fileOutMsfTmp);}
elsif ($formIn eq "msf") {
# shorten names
$kwd="msfShorten"; push(@kwdRmTmp,$kwd);
$fileOutMsfShorten=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_shorten";
($Lok,$msg)=
&msfShorten
($fileOutSeqTmp,$fileOutMsfShorten
); return(&errSbrMsg("failed shortening names msf=$fileOutSeqTmp->".
$fileOutMsfShorten.",msg=",$msg)) if (! $Lok);
# convert too to make sure compressing works
if ($doCompress){
$kwd=$formIn."-".$formOut; push(@kwdRmTmp,$kwd);
$fileOutMsfTmp=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_tmp";
($Lok,$msg)=
&msfCompress
($fileOutMsfShorten,$fileOutMsfTmp
); return(&errSbrMsg("failed compressing MSF=$fileOutSeqTmp->".
$fileOutMsfTmp."! msg=",$msg)) if (! $Lok);}
else {
$fileOutMsfTmp=$fileOutMsfShorten;}}
else {
return(&errSbr("input format=$formIn -> output=$formOut, not supported\n"));}
# ------------------------------
# (3) blow up when single sequence
if (&msfCountNali($fileOutMsfTmp) == 1){
$kwd=$formIn."-".$formOut."-addSelf";push(@kwdRmTmp,$kwd);
$fileOutMsfTmp2=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_tmpSelf";
($Lok,$msg)=
&msfBlowUp
($fileOutMsfTmp,$fileOutMsfTmp2
); return(0,"*** ERROR $sbrName: failed to write msf2 ($fileOutMsfTmp2)".
$msg."\n") if (! $Lok);
$fileOutMsfTmp=$fileOutMsfTmp2;}
# ------------------------------
# (4) now convert_seq to write HSSP
$cmd= ""; # eschew warnings
$an2= "N"; # write another format?
# gaps in master sequence as insertions?
$anIns= "N";
$anIns= "Y" if ($doCompress);
$anFormOut= "H"; # output = HSSP
$anId= " "; # specify id for master
# ------------------------------
# (5) convert to HSSP
$fileOutTmp=$fileOutLoc;
eval "\$cmd=\"$exeConvSeq,$fileOutMsfTmp,$anFormOut,$fileMatGcg,$anIns,$fileOutTmp,$anId,$an2\"";
# run FORTRAN script
# ($Lok,$msg)=&sysRunProg($cmd,0,"STDOUT");
($Lok,$msg)=&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
return(0,"*** ERROR $sbrName: failed to convert hssp to MSF\n".$msg."\n")
if (! $Lok || ! -e $fileOutTmp);
# ------------------------------
# (6) verify NALI in HSSP
$kwd=$formIn."-".$formOut."-correct";push(@kwdRmTmp,$kwd);
$fileOutHsspTmp=$file{$kwd}=$dirWork.$par{"titleTmp"}.".hssp_error";
($Lok,$msg)=&hsspCorrectNali($fileOutTmp,$fileOutHsspTmp,$fhSbr);
push(@fileOut,$fileOutTmp);}
# --------------------------------------------------
# MSF, FASTA, PIR, FASTAmul, PIRmul
elsif ($formOut eq "msf" || $formOut eq "fasta" || $formOut eq "pir" || $formOut eq "saf"
|| $formOut eq "fastamul" || $formOut eq "pirmul" || $formOut eq "gcg"){
# --------------------
# (1) convert MSF to SAF
if ($formIn eq "msf"){
$kwd=$formOut."-SAF";push(@kwdRmTmp,$kwd);
$fileOutSafTmp=$file{$kwd}=$dirWork.$par{"titleTmp"}.$kwd.$extOutLoc;
($Lok,$msg)=
&convMsf2saf
($fileInLoc,$fileOutSafTmp,$doCompress
); return(0,"*** ERROR $sbrName: failed to write saf ($fileOutSafTmp) ".
"from $fileInLoc".$msg."\n") if (! $Lok || ! -e $fileOutSafTmp);
$fileInLoc2=$fileOutSafTmp;}
else {
$fileInLoc2=$fileInLoc;}
# --------------------
if ($#beg>0){ # (2a) loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
$fragHere="$beg[$it]-$end[$it]";
if ($formIn eq "saf" || $formIn eq "msf"){
($Lok,$msg)=
&convSaf2many
($fileInLoc2,$fileOutTmp,$formOut,$fragHere,$extrLoc,
$fhSbr,$doCompress
); return(0,"*** ERROR $sbrName: failed to convert $fileInLoc2 to ".
"$formOut\n"."$msg\n") if (! $Lok);}
elsif ($formIn =~ /^fasta/){
($Lok,$msg)=
&convFastamul2many
($fileInLoc2,$fileOutTmp,$formOut,$fragHere,
$extrLoc,$fhSbr,$doCompress
); return(0,"*** ERROR $sbrName: failed to convert $fileInLoc2 to ".
"$formOut\n"."$msg\n") if (! $Lok);}
push(@fileOut,$fileOutTmp);}}
# --------------------
else {$fragHere=0; # (2b) no fragments
if ($formIn eq "saf" || $formIn eq "msf"){
($Lok,$msg)=
&convSaf2many
($fileInLoc2,$fileOutLoc,$formOut,$fragHere,
$extrLoc,$fhSbr,$doCompress
); return(0,"*** ERROR $sbrName: failed to convert $fileInLoc2 to ".
"$formOut\n".$msg."\n") if (! $Lok);}
elsif ($formIn =~ /^fasta/){
($Lok,$msg)=
&convFastamul2many
($fileInLoc2,$fileOutLoc,$formOut,$fragHere,
$extrLoc,$fhSbr,$doCompress
); return(0,"*** ERROR $sbrName: failed to convert $fileInLoc2 (fasta) ".
"to $formOut\n"."$msg\n") if (! $Lok);}
push(@fileOut,$fileOutLoc);}
}
else {
return(2,"*** ERROR $sbrName: output option $formOut not supported\n");}
# ------------------------------
# remove temporary files
if (! $par{"debug"}){
foreach $kwd(@kwdRmTmp){
if (-e $file{$kwd}){
print
"--- \t $sbrName: remove (",$file{$kwd},") \n"
if (defined $par{"verb2"} && $par{"verb2"});
unlink $file{$kwd};}}}
return(1,"ok $sbrName");
} # end of convAliGen
#===============================================================================
sub convDsspGen {
local($fileInLoc,$chainInLoc,$fileOutLoc,$formOut,$extOutLoc,$exeConvSeq,$fileMatGcg,
$frag,$fileScreenLoc,$dirWork,$fhSbr,$doSplitChainLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convDsspGen general converter for all DSSP in -> x
# in: for general info see 'convDsspGen'
# in: $fileInLoc file,dssp
# in: $chainLoc chain to extract
# in: $fileOut
# in: $formOut format_of_output_file
# in: $extOutLoc extension of expected output (fragments into _beg_end$extension)
# in: $exeConvSeq FORTRAN program convert_seq
# in: $fileMatGcg Maxhom_GCG.metric (for converting to HSSP)
# in: $frag fragments e.g. '1-5,10-100'
# in: $fileScreen output file for system commands
# in: $doSplitChain split chains when converting to FASTA
#
# out: converted file
#
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
#
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convDsspGen";$fhinLoc="FHIN"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def chainInLoc!") if (! defined $chainInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def frag!") if (! defined $frag);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
$doSplitChainLoc=0 if (! defined $doSplitChainLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
$chainIn=$chainInLoc; $chainIn="*" if (! $chainInLoc ||
length($chainInLoc)!=1 ||
$chainInLoc !~/[A-Z0-9]/);
# ------------------------------
$#kwdRmTmp=0; # temporary files
$fhSysRunProg=0;
$fhSysRunProg="STDOUT" if ($par{"verb2"});
$fileScreenLoc=0 if ($par{"debug"});
# ------------------------------
# chain over-rules fragments
if (($chainInLoc && $chainInLoc =~ /[A-Z0-9]/) ||
$doSplitChainLoc){
($Lok,%tmp)=
&dsspGetChain($fileInLoc);
return(0,"*** ERROR $sbrName: failed to extract chain from DSSP ($fileInLoc)\n")
if (! $Lok);
@tmp=split(/,/,$tmp{"chains"});
if ($doSplitChainLoc){
@chainLoc=@tmp;}
else {
$#chainLoc=0;}
undef %chainLoc;
foreach $it (1..$#tmp){
if (! $doSplitChainLoc && $tmp[$it] eq $chainInLoc){
$frag=$tmp{$chainInLoc,"beg"}."-".$tmp{$chainInLoc,"end"};
last;}
else {
$chainLoc{$tmp[$it],"beg"}=$tmp{$tmp[$it],"beg"};
$chainLoc{$tmp[$it],"end"}=$tmp{$tmp[$it],"end"};
}
}}
else {
$#chainLoc=0;}
$#beg=$#end=0; # ------------------------------
if ($frag){ # extract fragments?
@tmp=split(/,/,$frag);$#beg=$#end=0;
foreach $frag (@tmp){
next if ($frag !~ /\-/);$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
next if ($beg =~/\D/ || $end =~ /\D/);
push(@beg,$beg);push(@end,$end);}}
# ------------------------------
# FASTA/mul, PIR/mul, SAF/MSF
if ($formOut =~/^pir/ || $formOut =~/^fasta/ || $formOut =~/^msf/ || $formOut =~/^saf/ ){
# read entire DSSP sequence
($Lok,$seqSmallCap,$seqDssp)=
&dsspRdSeq($fileInLoc,$chainIn);
return(0,"*** ERROR $sbrName: failed to read dssp sequence for chain $chainIn\n".
$seqSmallCap."\n")
if (! $Lok || length($seqDssp)<5); # security margin for chainbreaks
# ******************************
# set fragment to zero!
if ($chainIn ne "*"){
$#beg=$#end=0 ;}
elsif ($#beg && $beg[1] > length($seqDssp)){
$#beg=$#end=0 ;}
elsif ($#beg && (1+$end[1]-$beg[1]) > length($seqDssp)){
$#beg=$#end=0 ;}
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
if (defined $chainIn && $chainIn && $chainIn ne "*" && length($chainIn)==1) {
$fileOutTmp=$fileOutLoc;
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g; # purge dir
$id.="_".$chainIn;}
else {
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/($extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g;} # purge dir
$seqDsspTmp=substr($seqDssp,$beg[$it],($end[$it]-$beg[$it]+1));
if (length($seqDsspTmp)<5){
print
"-*- WARN $sbrName: seq=$seqDsspTmp (beg=$beg[$it], end=$end[$it]) very short!\n";
next;}
($Lok,$msg)=
&seqGenWrt($seqDsspTmp,$id,$formOut,$fileOutTmp,$fhSbr);
return(0,"*** ERROR $sbrName: failed to write $formOut from DSSP\n"."$msg\n")
if (! $Lok || ! -e $fileOutTmp);
push(@fileOut,$fileOutTmp);}}
# loop over chains
elsif ($doSplitChainLoc){
foreach $chaintmp (@chainLoc){
$seqDsspTmp=
substr($seqDssp,
$chainLoc{$chaintmp,"beg"},
(1+$chainLoc{$chaintmp,"end"}-$chainLoc{$chaintmp,"beg"}));
# avoid duplicating identical chains
next if (defined $tmp{$seqDsspTmp});
$tmp{$seqDsspTmp}=1;
if (length($seqDsspTmp)<5){
print
"-*- WARN $sbrName: seq=$seqDsspTmp (beg=",
$chainLoc{$chaintmp,"beg"}," end=",$chainLoc{$chaintmp,"end"},") very short!\n";
next;}
if ($chaintmp !~ /^( |\*)$/ && length($chaintmp)==1){
$fileOutTmp=$fileOutLoc;
$id=$fileInLoc;
$id=~s/^.*\/|\..*$//g; # purge dir
$idnochain=$id;
$id.="_".$chaintmp;
$fileOutTmp=~s/$idnochain/$id/;}
else {
$fileOutTmp=$fileOutLoc;
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g;} # purge dir
($Lok,$msg)=
&seqGenWrt($seqDsspTmp,$id,$formOut,$fileOutTmp,$fhSbr);
return(0,"*** ERROR $sbrName: failed to write $formOut from DSSP\n"."$msg\n")
if (! $Lok || ! -e $fileOutTmp);
push(@fileOut,$fileOutTmp);}}
else {
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g; # purge dir
$id.="_".$chainIn if (defined $chainIn && $chainIn &&
$chainIn ne "*" && length($chainIn)==1);
($Lok,$msg)=
&seqGenWrt($seqDssp,$id,$formOut,$fileOutLoc,$fhSbr);
return(0,"*** ERROR $sbrName: failed to write $formOut from DSSP\n"."$msg\n")
if (! $Lok || ! -e $fileOutLoc);
push(@fileOut,$fileOutLoc);}
}
# ------------------------------
# HSSP
elsif ($formOut eq "hssp"){
# (1) read entire DSSP sequence
($Lok,$seqSmallCap,$seqDssp)=
&dsspRdSeq($fileInLoc,$chainIn);
return(0,"*** ERROR $sbrName: failed to read dssp sequence for chain $chainIn\n".
"$seqSmallCap\n")
if (! $Lok || length($seqDssp)<5); # security margin for chainbreaks
if ($#beg>0){ # (2a) loop over fragments
foreach $it (1..$#beg){
if (defined $chainIn && $chainIn && $chainIn ne "*" && length($chainIn)==1) {
$fileOutTmp=$fileOutLoc;
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g; # purge dir
$id.="_".$chainIn;}
else {
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/($extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g;} # purge dir
$seqDsspTmp=substr($seqDssp,$beg[$it],($end[$it]-$beg[$it]+1));
if (length($seqDsspTmp)<5){
print
"-*- WARN $sbrName: seq=$seqDsspTmp (beg=$beg[$it], end=$end[$it]) very short!\n";
next;}
# (3a) convert to MSF
$kwd="dssp-hssp"; push(@kwdRmTmp,$kwd);
$fileOutMsf=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_tmp";
($Lok,$msg)=
&seqGenWrt($seqDsspTmp,$id,"msf",$fileOutMsf,$fhSbr);
return(0,"*** ERROR $sbrName: failed to write MSF from DSSP\n"."$msg\n")
if (! $Lok || ! -e $fileOutMsf);
# (4a) blow up when single sequence
if (&msfCountNali($fileOutMsf) == 1){
$kwd=$formIn."-".$formOut."-addSelf";push(@kwdRmTmp,$kwd);
$fileOutMsfTmp2=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_tmpSelf";
($Lok,$msg)=
&msfBlowUp($fileOutMsf,$fileOutMsfTmp2);
return(0,"*** ERROR $sbrName: failed to write msf2 ($fileOutMsfTmp2)".
$msg."\n") if (! $Lok);
$fileOutMsf=$fileOutMsfTmp2;}
# (5a) now convert_seq to write HSSP
$cmd= ""; # eschew warnings
$an2= "N"; # write another format?
# gaps in master sequence as insertions?
$anIns= "N";
$anFormOut= "H"; # output = HSSP
$anId= " "; # specify id for master
eval "\$cmd=\"$exeConvSeq,$fileOutMsf,$anFormOut,$fileMatGcg,$anIns,$fileOutTmp,$anId,$an2\"";
# run FORTRAN script
($Lok,$msg)=
&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
return(0,"*** ERROR $sbrName: failed to convert DSSP -> MSF -> HSSP\n".$msg."\n")
if (! $Lok || ! -e $fileOutTmp);
push(@fileOut,$fileOutTmp);} }
else {
# (2b) no loop
if( $par{debug} ){ cluck("(2b) no loop"); }
$id=$fileInLoc;$id=~s/^.*\/|\..*$//g; # purge dir
$id.="_".$chainIn if (defined $chainIn && $chainIn && $chainIn ne "*" && length($chainIn)==1);
# (3a) convert to MSF
$kwd="dssp-hssp"; push(@kwdRmTmp,$kwd);
$fileOutMsf=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_tmp";
($Lok,$msg)=
&seqGenWrt($seqDssp,$id,"msf",$fileOutMsf,$fhSbr);
return(0,"*** ERROR $sbrName: failed to write MSF from DSSP\n"."$msg\n")
if (! $Lok || ! -e $fileOutMsf);
# (4a) blow up when single sequence
if (&msfCountNali($fileOutMsf) == 1){
$kwd=$formIn."-".$formOut."-addSelf";push(@kwdRmTmp,$kwd);
$fileOutMsfTmp2=$file{$kwd}=$dirWork.$par{"titleTmp"}.".msf_tmpSelf";
($Lok,$msg)=
&msfBlowUp($fileOutMsf,$fileOutMsfTmp2);
return(0,"*** ERROR $sbrName: failed to write msf2 ($fileOutMsfTmp2)".
$msg."\n") if (! $Lok);
$fileOutMsf=$fileOutMsfTmp2;}
# (5a) now convert_seq to write HSSP
$cmd= ""; # eschew warnings
$an2= "N"; # write another format?
# gaps in master sequence as insertions?
$anIns= "N";
$anFormOut= "H"; # output = HSSP
$anId= " "; # specify id for master
eval "\$cmd=\"$exeConvSeq,$fileOutMsf,$anFormOut,$fileMatGcg,$anIns,$fileOutLoc,$anId,$an2\"";
# run FORTRAN script
($Lok,$msg)=
&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
return(0,"*** ERROR $sbrName: failed to convert DSSP -> MSF -> HSSP\n".$msg."\n")
if (! $Lok || ! -e $fileOutMsf);
push(@fileOut,$fileOutLoc);} }
# ------------------------------
# unsupported output
# ------------------------------
else {
return(2,"*** ERROR $sbrName: output option $formOut not supported for FSSP\n");}
# ------------------------------
# remove temporary files
foreach $kwd(@kwdRmTmp){
if (-e $file{$kwd}){
print "--- \t $sbrName: remove (",$file{$kwd},") \n"
if (defined $par{"verb2"} && $par{"verb2"});
unlink $file{$kwd};}}
# clean up
undef %tmp; # slim-is-in
undef %chainLoc; # slim-is-in
$#chainLoc=0; # slim-is-in
return(1,"ok $sbrName");
} # end of convDsspGen
#===============================================================================
sub convFsspGen {
local($fileInLoc,$fileOutLoc,$formOut,$extOutLoc,$exeConvFssp2daf,$fileIncl,$dirDsspLoc,$dirWork,$fhSbr) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convFsspGen general converter for all FSSP in -> x
# in: for general info see 'convFsspGen'
# in: special:
# in: $fileIncl: contains ids to include, syntax PDBids + chain 1pdbC (or h|f|dssp files)
# out: converted file
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convFsspGen";$fhinLoc="FHIN_"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def exeConvFssp2daf!") if (! defined $exeConvFssp2daf);
return(0,"*** $sbrName: not def fileIncl!") if (! defined $fileIncl);
return(0,"*** $sbrName: not def dirDsspLoc!") if (! defined $dirDsspLoc);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
#return(0,"*** $sbrName: miss exe '$exeConvFssp2daf'!") if (! -e $exeConvFssp2daf && ! -l $exeConvFssp2daf);
return(0,"*** $sbrName: miss in file '$fileIncl'!") if ($fileIncl && ! -e $fileInLoc);
return(0,"*** $sbrName: miss dssp dir '$dirDsspLoc'!") if (! -d $dirDsspLoc);
# ------------------------------
# supported output options
$cmd= ""; # eschew warnings
$an2= "N"; # write another format?
# ------------------------------
if ($formOut eq "daf"){ # 2 daf
# --------------------
$#incl=0;$incl="unk"; # read include file
if ($fileIncl && -e $fileIncl){
open("$fhinLoc","$fileIncl") || confess( "failed to open $fileIncl: $!" ) ||
return(0,"*** $sbrName failed opening fileIn=$fileIncl\n");
$incl="";
while(<$fhinLoc>){next if (/^\#/);$_=~s/\n|\s//g;
next if (length($_)<3);
$_=~s/^.*\///g;$_=~s/\.[dhf]ssp[_!]*//g;
push(@incl,$_);$incl.="$_,";}close($fhinLoc);
$incl=~s/,$//g;}
$fileDafTmp=$dirWork.$par{"titleTmp"}."-fssp".$extOutLoc;
$Lok=
&convFssp2Daf($fileInLoc,$fileOutLoc,$fileDafTmp,$exeConvFssp2daf,$dirDsspLoc);
return(0,"*** ERROR $sbrName: failed to convert $fileInLoc to DAF $fileOutLoc, tmp=$fileDafTmp, ".
"exe=$exeConvFssp2daf\n") if (! $Lok || ! -e $fileOutLoc);
print
"--- \t $sbrName: remove ($fileDafTmp) \n" if (defined $par{"verb2"} && $par{"verb2"});
unlink $fileDafTmp;
push(@fileOut,$fileOutLoc);}
else {
return(2,"*** ERROR $sbrName: output option $formOut not supported for FSSP\n");}
return(1,"ok $sbrName");
} # end of convFsspGen
#===============================================================================
sub convHsspGen {
local($fileInLoc,$chainInLoc,$fileOutLoc,$formOut,$extOutLoc,$exeConvSeq,$exeConvHssp2saf,
$doExpand,$frag,$extrIn,$fileScreenLoc,$dirWork,$fhSbr,$doSplitChainLoc) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
if( $par{debug} ){ cluck(); }
#-------------------------------------------------------------------------------
# convHsspGen general converter for all HSSP in -> x
# in: $fileInLoc,$chainIn,$fileOutLoc,$formOut,$extOutLoc,$exeConvSeq,
# in: $doExpand,$frag,$extrIn,$dirWork,$fileScreenLoc,$fhSbr
# in: $fileInLoc file.hssp, file.out, format_of_output_file
# in: $fileOutLoc output file with converted sequence(s)
# in: NOTE: if many appended to @fileOut
# in: $formOut output format (lower caps)
# in: $extOutLoc extension of expected output (fragments into _beg_end$extension)
# in: $exeConvSeq the good old FORTRAN convert_seq
# in: $exeConvHssp2saf the new perl script doing it
# in: $doExpand do expand the deletions? (only for MSF)
# in: $frag fragments e.g. '1-5,10-100'
# in: $extrIn number of protein to extract
# in: $dirWork directory for temporary files
# in: $fileScreen file to dump convert_seq ..
# in: $fhSbr ERRORs of convert_seq
# in: $doSplitChain split chains when converting to FASTA
#
# out: converted file
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
#
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convHsspGen";$fhinLoc="FHIN"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
$chainInLoc="*" if (! defined $chainInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def exeConvSeq!") if (! defined $exeConvSeq);
return(0,"*** $sbrName: not def exeConvHssp2saf!") if (! defined $exeConvHssp2saf);
return(0,"*** $sbrName: not def doExpand!") if (! defined $doExpand);
return(0,"*** $sbrName: not def frag!") if (! defined $frag);
return(0,"*** $sbrName: not def extrIn!") if (! defined $extrIn);
return(0,"*** $sbrName: not def fileScreenLoc!") if (! defined $fileScreenLoc);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
$doSplitChainLoc=0 if (! defined $doSplitChainLoc);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
#return(0,"*** $sbrName: miss exe '$exeConvSeq'!") if (! -e $exeConvSeq && ! -l $exeConvSeq);
#return(0,"*** $sbrName: miss exe '$exeConvHssp2saf'!") if (! -e $exeConvHssp2saf && ! -l $exeConvHssp2saf);
$msgErr="";
$fhSysRunProg=0;
$fhSysRunProg="STDOUT" if ($par{"verb2"});
$fileScreenLoc=0 if ($par{"debug"});
# ------------------------------
# supported output options
if ($frag && $formOut eq "daf"){
print "-*- WARN $sbrName: fragment selection not supported for hssp->$formOut\n";
$frag=0;}
if ($doExpand && $formOut eq "daf"){
print "-*- WARN $sbrName: expansion of HSSP automatic (?) for hssp->$formOut\n";
$doExpand=0;}
# ------------------------------
# chain over-rules fragments
if ($chainInLoc && $chainInLoc =~ /[A-Z0-9]/){
($len,$ifir,$ilas)=
&hsspGetChainLength($fileInLoc,$chainInLoc);
# ignore!!!! for output which read only chains!!
if ($formOut !~ /^(pir|fasta)/){
$frag="$ifir-$ilas" if ($len>0); }
}
$#beg=$#end=0; # ------------------------------
if ($frag){ # extract fragments?
@tmp=split(/,/,$frag);$#beg=$#end=0;
foreach $frag(@tmp){next if ($frag !~ /\-/);$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
next if ($beg =~/\D/ || $end =~ /\D/);push(@beg,$beg);push(@end,$end);}}
$#kwdRmTmp=0; # temporary files
$cmd= ""; # eschew warnings
$an2= "N"; # write another format?
$anExpand= "N"; # expand sequences (i.e. fill in insertion list)
$anExpand= "Y" if ($doExpand);
# ------------------------------
if ($formOut eq "daf"){ # 2 daf
$anFormOut= "d";
$an1= "N"; # fragment? (if: prompted for two integers: beg end)
eval "\$cmd=\"$exeConvSeq,$fileInLoc,$anFormOut,$an1,$fileOutLoc,$an2\"";
# run FORTRAN script
($Lok,$msg)=&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
return(0,"*** ERROR $sbrName: failed to convert hssp to daf\n".$msg."\n")
if (! $Lok || ! -e $fileOutLoc);
push(@fileOut,$fileOutLoc);}
# ------------------------------
# MSF
elsif ($formOut eq "msf") {
$anFormOut= "m";
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
if ($formOut eq "saf"){
$kwd=$formOut.$it;
$fileOutTmp=$file{$kwd}=$dirWork.$par{"titleTmp"}.$kwd.$extOutLoc;
push(@kwdRmTmp,$kwd);}
else {
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;}
$an1= "Y"; # fragment? (if: prompted for two integers: beg end)
$anF= "$beg[$it] $end[$it]"; # answer for fragment
eval "\$cmd=\"$exeConvSeq,$fileInLoc,$anFormOut,$an1,$anF,$fileOutTmp,$anExpand,$an2\"";
# run FORTRAN script
($Lok,$msg)=&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
$msgErr.="*** ERROR $sbrName: failed to convert hssp to MSF frag $it \n".$msg."\n"
if (! $Lok || ! -e $fileOutTmp);
push(@fileOut,$fileOutTmp);}
return(0,$msgErr) if ($msgErr =~ /ERROR/);}
else {
$an1= "N"; # fragment? (if: prompted for two integers: beg end)
$fileOutTmp=$fileOutLoc;
eval "\$cmd=\"$exeConvSeq,$fileInLoc,$anFormOut,$an1,$fileOutTmp,$anExpand,$an2\"";
# run FORTRAN script
($Lok,$msg)=&sysRunProg($cmd,$fileScreenLoc,$fhSysRunProg);
return(0,"*** ERROR $sbrName: failed to convert hssp to MSF\n".$msg."\n")
if (! $Lok || ! -e $fileOutTmp);
push(@fileOut,$fileOutTmp);}}
# ------------------------------
# SAF
elsif ($formOut eq "saf" ){
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
@tmp=($fileInLoc,"fileOut=$fileOutTmp");
push(@tmp,"frag=$beg[$it]-$end[$it]");
push(@tmp,"extr=$extrIn") if (defined $extrIn && $extrIn);
push(@tmp,"expand") if ($doExpand);
push(@tmp,"debug") if (! $fileScreenLoc);
# call package
($Lok,$msg)=&conv_hssp2saf::conv_hssp2saf(@tmp);
$msgErr.="*** ERROR $sbrName: failed to convert hssp to SAF frag $it \n".$msg."\n"
if (! $Lok || ! -e $fileOutTmp);
push(@fileOut,$fileOutTmp);}
return(0,$msgErr) if ($msgErr =~ /ERROR/);}
else {
$fileOutTmp=$fileOutLoc;
@tmp=($fileInLoc,"fileOut=$fileOutTmp");
push(@tmp,"extr=$extrIn") if (defined $extrIn && $extrIn);
push(@tmp,"expand") if ($doExpand);
push(@tmp,"debug") if (! $fileScreenLoc);
# call package
($Lok,$msg)=&conv_hssp2saf::conv_hssp2saf(@tmp);
return(0,"*** ERROR $sbrName: failed to convert hssp to Saf\n".$msg."\n")
if (! $Lok || ! -e $fileOutTmp);
push(@fileOut,$fileOutTmp);}}
# ------------------------------
# FASTA/PIR mul
elsif ($formOut eq "pirmul" || $formOut eq "fastamul"
|| $formOut eq "fasta" || $formOut eq "pir" ){
$anFormOut= substr($formOut,1,1);
$Lone=$extr=0; # extract only some sequences?
if ($formOut eq "fasta" || $formOut eq "pir" ){
$Lone=1;$extr=$extrIn;$extr=1 if (! defined $extr || $extr < 1);}
$extr="guide" if ($Lone);
# --------------------
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
$fragTmp=$beg[$it]."-".$end[$it];
# sbr call
($Lok,$msg)=
&convHssp2seq($fileInLoc,$chainInLoc,$fileOutTmp,$formOut,$extOutLoc,
$doExpand,$fragTmp,$extr,0,0,0,0,$fhSbr);
return(&errSbrMsg("failed HSSP -> $formOut (sbr)",$msg)) if (! $Lok);
# no output -> skip
if (! -e $fileOutTmp){
$msgErr.="*** ERROR $sbrName: failed to convert hssp to $formOut frag $it\n";
next; }
# extract particular sequence
push(@fileOut,$fileOutTmp); } }
# --------------------
else { # NO fragment
$fileOutTmp=$fileOutLoc;
$fragTmp=0;
# sbr call
($Lok,$msg)=
&convHssp2seq($fileInLoc,$chainInLoc,$fileOutTmp,$formOut,$extOutLoc,
$doExpand,$fragTmp,$extr,0,0,0,0,$fhSbr,$doSplitChainLoc);
return(&errSbrMsg("failed HSSP -> $formOut (sbr)",$msg)) if (! $Lok || ! -e $fileOutTmp);
# extract particular sequence
push(@fileOut,$fileOutTmp); } }
else {
return(2,"*** ERROR $sbrName: output option $formOut not supported for HSSP\n");}
# ------------------------------
# remove temporary files
foreach $kwd(@kwdRmTmp){
if (-e $file{$kwd}){
print "--- \t $sbrName: remove (",$file{$kwd},") \n"
if (defined $par{"verb2"} && $par{"verb2"});
unlink $file{$kwd};}}
return(1,"ok $sbrName");
} # end of convHsspGen
#===============================================================================
sub convPirmulGen {
local($fileInLoc,$fileOutLoc,$formOut,$extOutLoc,$frag,$extrIn,$dirWork,$fhSbr) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convPirmulGen general converter for all PIRMUL in -> x
# in: for general info see 'convPirmulGen'
# out: converted file
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convPirmulGen";$fhinLoc="FHIN"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def frag!") if (! defined $frag);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
# ------------------------------
$#kwdRmTmp=0; # temporary files
$#beg=$#end=0; # ------------------------------
if ($frag){ # extract fragments?
@tmp=split(/,/,$frag);$#beg=$#end=0;
foreach $frag(@tmp){next if ($frag !~ /\-/);$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
next if ($beg =~/\D/ || $end =~ /\D/);push(@beg,$beg);push(@end,$end);}}
# ------------------------------
# only to FASTA and FASTAmul
if ($formOut eq "fasta" || $formOut eq "fastamul" ){
$Lone=$extr=0; # extract only some sequences?
if ($formOut eq "fasta"){
$Lone=1;$extr=$extrIn;$extr=1 if (! defined $extr || $extr < 1);}
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
$fragHere="$beg[$it]-$end[$it]";
($Lok,$msg)=
&convPir2fasta($fileInLoc,$fileOutTmp,$fragHere,$extr);
return(0,"*** ERROR $sbrName: failed to convert pirmul to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutTmp);}}
else {$fragHere=0;
($Lok,$msg)=
&convPir2fasta($fileInLoc,$fileOutLoc,$fragHere,$extr);
return(0,"*** ERROR $sbrName: failed to convert pirmul to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutLoc);}}
else {
return(2,"*** ERROR $sbrName: output option $formOut not supported for FSSP\n");}
return(1,"ok $sbrName");
} # end of convPirmulGen
#===============================================================================
sub convSeqGen {
local($fileInLoc,$fileOutLoc,$formIn,$formOut,$extOutLoc,
$exeConvSeq,$frag,$fileScreenLoc,$dirWork,$fhSbr) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convSeqGen general converter for all sequence formats into -> x
# in: for general info see 'convSeqGen'
# out: converted file
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convSeqGen";$fhinLoc="FHIN"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formIn!") if (! defined $formIn);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def exeConvSeq!") if (! defined $exeConvSeq);
return(0,"*** $sbrName: not def frag!") if (! defined $frag);
return(0,"*** $sbrName: not def fileScreenLoc!") if (! defined $fileScreenLoc);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
#return(0,"*** $sbrName: miss exe '$exeConvSeq'!") if (! -e $exeConvSeq && ! -l $exeConvSeq);
$#beg=$#end=0; # ------------------------------
if ($frag){ # extract fragments?
@tmp=split(/,/,$frag);$#beg=$#end=0;
foreach $frag(@tmp){
next if ($frag !~ /\-/);$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
next if ($beg =~/\D/ || $end =~ /\D/);push(@beg,$beg);push(@end,$end);}}
# ------------------------------
# only sequence formats
if ($formOut eq "fasta" || $formOut eq "pir" || $formOut eq "gcg"){
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
$fragHere="$beg[$it]-$end[$it]";
($Lok,$msg)=
&convSeq2seq($fileInLoc,$formIn,$fileOutTmp,$formOut,$fragHere,$fileScreenLoc,$fhSbr);
# ($Lok,$msg)=
# &convSeq2seqOld($exeConvSeq,$fileInLoc,$fileOutTmp,$formOut,$fragHere,$fileScreenLoc,$fhSbr);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutTmp);}}
else {$fragHere=0;
($Lok,$msg)=
&convSeq2seq($fileInLoc,$formIn,$fileOutLoc,$formOut,$fragHere,$fileScreenLoc,$fhSbr);
# ($Lok,$msg)=
# &convSeq2seqOld($exeConvSeq,$fileInLoc,$fileOutLoc,$formOut,$fragHere,$fileScreenLoc,$fhSbr);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutLoc);}}
# ------------------------------
# convert to SAF
elsif ($formOut eq "saf" && $formIn eq "fasta"){
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
($Lok,$id,$seq)=&fastaRdGuide($fileInLoc);
$tmp{"seq","1"}=substr($seq,$beg[$it],($end[$it]-$beg[$it]+1));
$tmp{"NROWS"}= 1;$tmp{"id","1"}= $id;
($Lok,$msg)=&safWrt($fileOutTmp,%tmp);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutTmp);}}
else {$fragHere=0;
($Lok,$id,$tmp{"seq","1"})=
&fastaRdGuide($fileInLoc);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
$id=~s/^(\S+).*$/$1/;
$tmp{"NROWS"}= 1;$tmp{"id","1"}= $id;
($Lok,$msg)=&safWrt($fileOutLoc,%tmp);
return(0,"*** ERROR $sbrName: failed to convert fasta to $formOut\n"."$msg\n") if (! $Lok);
push(@fileOut,$fileOutLoc);}}
else {
return(2,"*** ERROR $sbrName: output option $formOut not supported for $formIn\n");}
return(1,"ok $sbrName");
} # end of convSeqGen
#===============================================================================
sub convPdbGen {
local($fileInLoc,$chainInLoc,$fileOutLoc,$formOut,$extOutLoc,$frag,$dirWork,$fhSbr) = @_ ;
local($sbrName,$fhinLoc,$tmp,$Lok);
$[ =1 ;
#-------------------------------------------------------------------------------
# convPdbGen general converter for all sequence formats into -> x
# in: for general info see 'convPdbGen'
# out: converted file
# out GLOBAL: @fileOut,@kwdRm,$file{"kwd"} files to remove
# err: 0,$msg -> unspecified error
# err: 1,$msg -> ok
# err: 2,$msg -> conversion option not supported
#-------------------------------------------------------------------------------
$sbrName="$scrName:"."convPdbGen";$fhinLoc="FHIN"."$sbrName";
# ------------------------------
# check arguments
return(0,"*** $sbrName: not def fileInLoc!") if (! defined $fileInLoc);
return(0,"*** $sbrName: not def chainInLoc!") if (! defined $chainInLoc);
return(0,"*** $sbrName: not def fileOutLoc!") if (! defined $fileOutLoc);
return(0,"*** $sbrName: not def formOut!") if (! defined $formOut);
return(0,"*** $sbrName: not def extOutLoc!") if (! defined $extOutLoc);
return(0,"*** $sbrName: not def frag!") if (! defined $frag);
return(0,"*** $sbrName: not def dirWork!") if (! defined $dirWork);
$fhSbr="STDOUT" if (! defined $fhSbr);
return(0,"*** $sbrName: miss in file '$fileInLoc'!") if (! -e $fileInLoc);
$#beg=$#end=0; # ------------------------------
if ($frag){ # extract fragments?
@tmp=split(/,/,$frag);$#beg=$#end=0;
foreach $frag(@tmp){
next if ($frag !~ /\-/);$frag=~s/\s//g;
($beg,$end)=split('-',$frag);
next if ($beg =~/\D/ || $end =~ /\D/);push(@beg,$beg);push(@end,$end);}}
# ------------------------------
# PDB
return(2,"*** ERROR $sbrName: output option $formOut not supported for $formIn\n")
if ($formOut !~/^(fasta|pir|gcg)/);
if ($#beg>0){ # loop over fragments
foreach $it (1..$#beg){
$fileOutTmp=$fileOutLoc;$fileOutTmp=~s/(\.$extOutLoc)/\_$beg[$it]\_$end[$it]$1/;
# read sequence
($Lok,$msg)=
&convPdb2seq($fileInLoc,$chainInLoc,$fileOutTmp,$formOut,$fragHere,$fhSbr);
return(0,"*** ERROR $sbrName: failed to convert PDB to $formOut\n".
"$msg\n") if (! $Lok);
push(@fileOut,$fileOutTmp);}}
else {
$fragHere=0;
($Lok,$msg)=
&convPdb2seq($fileInLoc,$chainInLoc,$fileOutLoc,$formOut,$fragHere,$fhSbr);
return(0,"*** ERROR $sbrName: failed to convert PDB to $formOut\n".
"$msg\n") if (! $Lok);
push(@fileOut,$fileOutLoc); }
return(1,"ok $sbrName");
} # end of convPdbGen
#===============================================================================
sub wrtLoc {
local($fhLoc)=@_;
$[ =1 ;
#-------------------------------------------------------------------------------
# wrtLoc write onto screen where we are
#-------------------------------------------------------------------------------
# for many files to convert: do time estimate
if ($nfileIn > 10) {
$estimate=
&fctRunTimeLeft($timeBeg,$nfileIn,$itFile);
$estimate="?" if ($itFile < 5);
$tmp= sprintf("%4d (%4.1f%-1s), time left=%-s",
$itFile,(100*$itFile/$nfileIn),"%",$estimate); }
else {
$tmp="file no=".$itFile; }
$tmpWrt= "$formIn -> $formOut: $fileIn -> $fileOutDef ";
$tmpWrt.=$tmp;
if( $par{debug} ){ print $fhLoc "$tmpWrt\n"; }
} # end of wrtLoc
1;
# vim:et:ai:
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