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# BioPerl module for Bio::Tools::Run::Alignment::DBA
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Alignment::DBA - Object for the alignment of two
sequences using the DNA Block Aligner program.
=head1 SYNOPSIS
use Bio::Tools::Run::Alignment::DBA;
# Build a dba alignment factory
my @params = ('matchA' => 0.75,
'matchB' => '0.55',
'dymem' =>'linear');
my $factory = Bio::Tools::Run::Alignment::DBA->new(@params);
# Pass the factory a filename with 2 sequences to be aligned.
$inputfilename = 't/data/dbaseq.fa';
# @hsps is an array of GenericHSP objects
my @hsps = $factory->align($inputfilename);
# or
my @files = ('t/data/dbaseq1.fa','t/data/dbaseq2.fa');
my @hsps = $factory->align(\@files);
# or where @seq_array is an array of Bio::Seq objects
$seq_array_ref = \@seq_array;
my @hsps = $factory->align($seq_array_ref);
=head1 DESCRIPTION
DNA Block Aligner program (DBA) was developed by Ewan Birney. DBA
is part of the Wise package available at
L<http://www.sanger.ac.uk/software/wise2>.
You will need to enable dba to find the dba program. This can
be done in a few different ways:
1. Define an environmental variable WISEDIR:
export WISEDIR =/usr/local/share/wise2.2.0
2. Include a definition of an environmental variable WISEDIR in
every script that will use DBA.pm:
$ENV{WISEDIR} = '/usr/local/share/wise2.2.20';
3. Make sure that the dba application is in your PATH.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Alignment::DBA;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@DBA_SWITCHES @DBA_PARAMS @OTHER_SWITCHES %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::SimpleAlign;
use Bio::AlignIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use Bio::Search::HSP::GenericHSP;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
@DBA_PARAMS = qw(MATCHA MATCHB MATCHC MATCHD GAP BLOCKOPEN UMATCH SINGLE
NOMATCHN PARAMS KBYTE DYMEM DYDEBUG ERRORLOG);
@OTHER_SWITCHES = qw(OUTFILE);
@DBA_SWITCHES = qw(HELP SILENT QUIET ERROROFFSTD ALIGN LABEL);
# Authorize attribute fields
foreach my $attr ( @DBA_PARAMS, @DBA_SWITCHES,
@OTHER_SWITCHES) { $OK_FIELD{$attr}++; }
}
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'dba';
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{WISEDIR},"/src/bin") if $ENV{WISEDIR};
}
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/'PROGRAM'/i ) {
$self->executable($value);
next;
}
$self->$attr($value);
}
return $self;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 version
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($self) = @_;
my $exe = $self->executable();
return undef unless defined $exe;
my $string = `$exe -- ` ;
$string =~ /\(([\d.]+)\)/;
return $1 || undef;
}
=head2 align
Title : align
Usage :
$inputfilename = 't/data/seq.fa';
@hsps = $factory->align($inputfilename);
or
#@seq_array is array of Seq objs
$seq_array_ref = \@seq_array;
@hsps = $factory->align($seq_array_ref);
or
my @files = ('t/data/seq1.fa','t/data/seq2.fa');
@hsps = $factory->align(\@files);
Function: Perform a DBA alignment
Returns : An array of Bio::Search::HSP::GenericHSP objects
Args : Name of a file containing a set of 2 fasta sequences
or else a reference to an array to 2 Bio::Seq objects.
or else a reference to an array of 2 file
names containing 1 fasta sequence each
Throws an exception if argument is not either a string (eg a
filename) or a reference to an array of 2 Bio::Seq objects. If
argument is string, throws exception if file corresponding to string
name can not be found. If argument is Bio::Seq array, throws
exception if less than two sequence objects are in array.
=cut
sub align {
my ($self,$input) = @_;
my ($temp,$infile1, $infile2, $seq);
my ($attr, $value, $switch);
# Create input file pointer
($infile1,$infile2)= $self->_setinput($input);
if (!($infile1 && $infile2)) {$self->throw("Bad input data (sequences need an id ) or less than 2 sequences in $input !");}
# Create parameter string to pass to dba program
my $param_string = $self->_setparams();
# run dba
my @hsps = $self->_run($infile1,$infile2,$param_string);
return @hsps;
}
#################################################
=head2 _run
Title : _run
Usage : Internal function, not to be called directly
Function: makes actual system call to dba program
Example :
Returns : nothing; dba output is written to a temp file
Args : Name of a file containing a set of unaligned fasta sequences
and hash of parameters to be passed to dba
=cut
sub _run {
my ($self,$infile1,$infile2,$param_string) = @_;
my $instring;
$self->debug( "Program ".$self->executable."\n");
unless( $self->outfile){
my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir);
close($tfh);
undef $tfh;
$self->outfile($outfile);
}
my $outfile = $self->outfile();
my $commandstring = $self->executable." $param_string -pff $infile1 $infile2 > $outfile";
$self->debug( "dba command = $commandstring");
my $status = system($commandstring);
$self->throw( "DBA call ($commandstring) crashed: $? \n") unless $status==0;
#parse pff format and return a Bio::Search::HSP::GenericHSP array
my $hsps = $self->_parse_results($outfile);
return @{$hsps};
}
=head2 _parse_results
Title : __parse_results
Usage : Internal function, not to be called directly
Function: Parses dba output
Example :
Returns : an reference to an array of GenericHSPs
Args : the name of the output file
=cut
sub _parse_results {
my ($self,$outfile) = @_;
$outfile||$self->throw("No outfile specified");
my ($start,$end,$name,$seqname,$seq,$seqchar,$tempname,%align);
my $count = 0;
my @hsps;
open(OUT,$outfile);
my (%query,%subject);
while(my $entry = <OUT>){
if($entry =~ /^>(.+)/ ) {
$tempname = $1;
if( defined $name ) {
if($count == 0){
my @parse = split("\t",$name);
$query{seqname} = $parse[0];
$query{start} = $parse[3];
$query{end} = $parse[4];
$query{score} = $parse[5];
$query{strand} = ($parse[6] eq '+') ? 1 : -1;
my @tags = split(";",$parse[8]);
foreach my $tag(@tags){
$tag =~/(\S+)\s+(\S+)/;
$query{$1} = $2;
}
$query{seq} = $seqchar;
$count++;
}
elsif ($count == 1){
my @parse = split("\t",$name);
$subject{seqname} = $parse[0];
$subject{start} = $parse[3];
$subject{end} = $parse[4];
$subject{score} = $parse[5];
$subject{strand} = ($parse[6] eq '+') ? 1:-1;
my @tags = split(";",$parse[8]);
foreach my $tag(@tags){
$tag =~/(\S+)\s+(\S+)/;
$subject{$1} = $2;
}
$subject{seq} = $seqchar;
#create homology string
my $xor = $query{seq}^$subject{seq};
my $identical = $xor=~tr/\c@/*/;
$xor=~tr/*/ /c;
my $hsp= Bio::Search::HSP::GenericHSP->new(-algorithm =>'DBA',
-score =>$query{score},
-hsp_length =>length($query{seq}),
-query_gaps =>$query{gaps},
-hit_gaps =>$subject{gaps},
-query_name =>$query{seqname},
-query_start =>$query{start},
-query_end =>$query{end},
-hit_name =>$subject{seqname},
-hit_start =>$subject{start},
-hit_end =>$subject{end},
-hit_length =>length($self->_subject_seq->seq),
-query_length =>length($self->_query_seq->seq),
-query_seq =>$query{seq},
-hit_seq =>$subject{seq},
-conserved =>$identical,
-identical =>$identical,
-homology_seq =>$xor);
push @hsps, $hsp;
$count = 0;
}
}
$name = $tempname;
$seqchar = "";
next;
}
$entry =~ s/[^A-Za-z\.\-]//g;
$seqchar .= $entry;
}
#do for the last entry
if($count == 1){
my @parse = split("\t",$name);
$subject{seqname} = $parse[1];
$subject{start} = $parse[3];
$subject{end} = $parse[4];
$subject{score} = $parse[5];
$subject{strand} = ($parse[6] eq '+') ? 1:-1;
my @tags = split(";",$parse[8]);
foreach my $tag(@tags){
$tag =~/(\S+)\s+(\S+)/;
$subject{$1} = $2;
}
$subject{seq} = $seqchar;
#create homology string
my $xor = $query{seq}^$subject{seq};
my $identical = $xor=~tr/\c@/*/;
$xor=~tr/*/ /c;
my $hsp= Bio::Search::HSP::GenericHSP->new(-algorithm =>'DBA',
-score =>$query{score},
-hsp_length =>length($query{seq}),
-query_gaps =>$query{gaps},
-hit_gaps =>$subject{gaps},
-query_name =>$query{seqname},
-query_start =>$query{start},
-query_end =>$query{end},
-hit_name =>$subject{seqname},
-hit_start =>$subject{start},
-hit_end =>$subject{end},
-hit_length =>length($self->_subject_seq->seq),
-query_length =>length($self->_query_seq->seq),
-query_seq =>$query{seq},
-hit_seq =>$subject{seq},
-conserved =>$identical,
-identical =>$identical,
-homology_seq =>$xor);
push @hsps, $hsp;
}
return \@hsps;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: Create input file for dba program
Example :
Returns : name of file containing dba data input
Args : Seq or Align object reference or input file name
=cut
sub _setinput {
my ($self, $input, $suffix) = @_;
my ($infilename, $seq, $temp, $tfh1,$tfh2,$outfile1,$outfile2);
#there is gotta be some repetition here...need to clean up
if (ref($input) ne "ARRAY"){ #a single file containg 2 seqeunces
$infilename = $input;
unless(-e $input){return 0;}
my $in = Bio::SeqIO->new(-file => $infilename , '-format' => 'Fasta');
($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);
my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'Fasta','-flush'=>1);
my $out2 = Bio::SeqIO->new(-fh=> $tfh2 , '-format' => 'Fasta','-flush'=>1);
my $seq1 = $in->next_seq() || return 0;
my $seq2 = $in->next_seq() || return 0;
$out1->write_seq($seq1);
$out2->write_seq($seq2);
$self->_query_seq($seq1);
$self->_subject_seq($seq2);
$out1->close();
$out2->close();
close($tfh1);
close($tfh2);
undef $tfh1;
undef $tfh2;
return $outfile1,$outfile2;
}
else {
scalar(@{$input}) == 2 || $self->throw("dba alignment can only be run on 2 sequences not.");
if(ref($input->[0]) eq ""){#passing in two file names
my $in1 = Bio::SeqIO->new(-file => $input->[0], '-format' => 'fasta');
my $in2 = Bio::SeqIO->new(-file => $input->[1], '-format' => 'fasta');
($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);
my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'fasta');
my $out2 = Bio::SeqIO->new(-fh=> $tfh2 , '-format' => 'fasta');
my $seq1 = $in1->next_seq() || return 0;
my $seq2 = $in2->next_seq() || return 0;
$out1->write_seq($seq1);
$out2->write_seq($seq2);
$self->_query_seq($seq1);
$self->_subject_seq($seq2);
close($tfh1);
close($tfh2);
undef $tfh1;
undef $tfh2;
return $outfile1,$outfile2;
}
elsif($input->[0]->isa("Bio::PrimarySeqI") && $input->[1]->isa("Bio::PrimarySeqI")) {
($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
($tfh2,$outfile2) = $self->io->tempfile(-dir=>$self->tempdir);
my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'fasta');
my $out2 = Bio::SeqIO->new(-fh=> $tfh2 , '-format' => 'fasta');
$out1->write_seq($input->[0]);
$out2->write_seq($input->[1]);
$self->_query_seq($input->[0]);
$self->_subject_seq($input->[1]);
close($tfh1);
close($tfh2);
undef $tfh1;
undef $tfh2;
return $outfile1,$outfile2;
}
else {
return 0;
}
}
return 0;
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for dba program
Example :
Returns : parameter string to be passed to dba
during align or profile_align
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
$self = shift;
my $param_string = "";
for $attr ( @DBA_PARAMS ) {
$value = $self->$attr();
next unless (defined $value);
# next if $attr =~/outfile/i;
my $attr_key = lc $attr; #put params in format expected by dba
if($attr_key =~ /match([ABCDabcd])/i){
$attr_key = "match".uc($1);
}
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key.' '.$value;
}
for $attr ( @DBA_SWITCHES) {
$value = $self->$attr();
next unless ($value);
my $attr_key = lc $attr; #put switches in format expected by dba
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key ;
}
return $param_string;
}
=head2 _query_seq()
Title : _query_seq
Usage : Internal function, not to be called directly
Function: get/set for the query sequence
Example :
Returns :
Args :
=cut
sub _query_seq {
my ($self,$seq) = @_;
if(defined $seq){
$self->{'_query_seq'} = $seq;
}
return $self->{'_query_seq'};
}
=head2 _subject_seq()
Title : _subject_seq
Usage : Internal function, not to be called directly
Function: get/set for the subject sequence
Example :
Returns :
Args :
=cut
sub _subject_seq {
my ($self,$seq) = @_;
if(defined $seq){
$self->{'_subject_seq'} = $seq;
}
return $self->{'_subject_seq'};
}
1; # Needed to keep compiler happy
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