/usr/share/perl5/Bio/Tools/Run/Coil.pm is in libbio-perl-run-perl 1.7.1-3.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 | # Wrapper module for Coil Bio::Tools::Run::Coil
#
# Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
# originally written by Marc Sohrmann (ms2@sanger.ac.uk)
# Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Coil - wrapper for ncoils program
=head1 SYNOPSIS
# Build a Coil factory
my $factory = Bio::Tools::Run::Coil->new($params);
# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);
=head1 DESCRIPTION
This module is a wrapper for the B<ncoils> program available via
L<http://www.russell.embl-heidelberg.de/coils/coils.tar.gz> for predicting
coiled coils in protein sequences.
By default it looks for an executable called I<ncoils> and data/parameter files
in the directory specified by the I<COILSDIR> environmental variable.
=head1 REFERENCES
Lupas, van Dyke & Stock,
I<Predicting coiled coils from protein sequences>,
Science B<252>:1162-1164, 1991.
Lupas, A.,
I<Prediction and Analysis of Coiled-Coil Structures>,
Meth. Enzymology B<266>:513-525, 1996.
=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 AUTHORS
Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
originally written by Marc Sohrmann (ms2@sanger.ac.uk)
Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
Cared for by the Fugu Informatics team (fuguteam@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::Coil;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR
$PROGRAMNAME @COIL_PARAMS %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Coil;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
@COIL_PARAMS=qw(PROGRAM VERBOSE QUIET SILENT);
foreach my $attr ( @COIL_PARAMS)
{ $OK_FIELD{$attr}++; }
}
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 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'ncoils';
}
=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{COILSDIR}) if $ENV{COILSDIR};
}
=head2 new
Title : new
Usage : $coil->new(@params)
Function: creates a new Coil factory
Returns: Bio::Tools::Run::Coil
Args :
=cut
sub new {
my ($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;
}
=head2 predict_protein_features
Title : predict_protein_features()
Usage : DEPRECATED. Use $obj->run instead.
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
=cut
sub predict_protein_features{
return shift->run(@_);
}
=head2 run
Title : run
Usage : $obj->run($seq)
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI, or a Fasta filename.
=cut
sub run{
my ($self,$seq) = @_;
my @feats;
if (ref($seq) ) { # it is an object
if (ref($seq) =~ /GLOB/) {
$self->throw("cannot use filehandle");
}
my $infile1 = $self->_writeSeqFile($seq);
$self->_input($infile1);
@feats = $self->_run();
unlink $infile1;
}
else {
#The argument is not a seq object but a sequence in a fasta file.
#Perhaps should check here or before if this file is fasta format...if not die
#Here the file does not need to be created or deleted. Its already written and may be used by other runnables.
$self->_input($seq);
@feats = $self->_run();
}
return @feats;
}
=head2 _input
Title : _input
Usage : obj->_input($seqFile)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub _input() {
my ($self,$infile1) = @_;
if(defined $infile1){
$self->{'input'}=$infile1;
}
return $self->{'input'};
}
=head2 _run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An array of Bio::SeqFeature::Generic objects
Args :
=cut
sub _run {
my ($self)= @_;
my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
my $str =$self->executable." -f < ".$self->{'input'}." > ".$outfile;
if($self->quiet || $self->verbose <=0 || $self->silent){
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$str.=" 2>$null";
}
my $status = system($str);
$self->throw( "Coil call ($str) crashed: $? \n") unless $status==0;
my $coil_parser = Bio::Tools::Coil->new();
my $filehandle;
if (ref ($outfile) !~ /GLOB/) {
open (COIL, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
$filehandle = \*COIL;
}
else {
$filehandle = $outfile;
}
my @coil_feat;
while(my $coil_feat = $coil_parser->next_result($filehandle)){
push @coil_feat, $coil_feat;
}
$self->cleanup();
close($tfh1);
undef $tfh1;
unlink $outfile;
return @coil_feat;
}
=head2 _writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub _writeSeqFile{
my ($self,$seq) = @_;
my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir());
my $in = Bio::SeqIO->new(-fh => $tfh , '-format' => 'Fasta');
$in->write_seq($seq);
return $inputfile;
}
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