Raw content of Bio::Tools::Coil
<![CDATA[# Parser module for Coil Bio::Tools::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>
# 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::Coil
=head1 SYNOPSIS
use Bio::Tools::Coil
my $parser = new Bio::Tools::Coil();
while( my $sp_feat = $parser->next_result($file) ) {
#do something
#eg
push @sp_feat, $sp_feat;
}
=head1 DESCRIPTION
Parser for Coil output
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR
Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
originally written by Marc Sohrmann (ms2@sanger.ac.uk)
Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::Tools::Coil;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::SeqFeature::FeaturePair;
use Bio::Root::IO;
use Bio::SeqFeature::Generic;
@ISA = qw(Bio::Root::Root Bio::Root::IO);
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 parse_results
Title : parse_results
Usage : obj->parse_results
Function: Parses the coil output. Automatically called by
next_result() if not yet done.
Example :
Returns :
=cut
sub parse_results {
my ($self,$resfile) = @_;
my $filehandle = $resfile;
my %result_hash =_read_fasta($filehandle);#bala no file handle
my @ids = keys %result_hash;
my @feats;
foreach my $id (keys %result_hash){
my $pep = reverse ($result_hash{$id});
my $count = my $switch = 0;
my ($start, $end);
while (my $aa = chop $pep) {
$count++;
if (!$switch && $aa eq "x") {
$start = $count;
$switch = 1;
}
elsif ($switch && $aa ne "x") {
$end = $count-1;
my (%feature);
$feature{name} = $id;
$feature{start} = $start;
$feature{end} = $end;
$feature{source} = "Coils";
$feature{primary} = 'ncoils';
($feature{program}) = 'ncoils';
$feature{logic_name} = 'Coils';
my $new_feat = $self->create_feature (\%feature);
$self->_add_prediction($new_feat);
$switch = 0;
}
}
}
$self->_predictions_parsed(1);
}
=head2 next_result
Title : next_result
Usage : while($feat = $coil->next_result($file)) {
# do something
}
Function: Returns the next protein feature of the coil output file
Returns :
Args :
=cut
sub next_result{
my ($self,$resfile) = @_;
my $gene;
$self->parse_results($resfile) unless $self->_predictions_parsed();
$gene = $self->_result();
return $gene;
}
=head2 _result
Title : _result
Usage : $feat = $obj->_result()
Function: internal
Example :
Returns :
=cut
sub _result{
my ($self) = @_;
return undef unless(exists($self->{'_feats'}) && @{$self->{'_feats'}});
return shift(@{$self->{'_feats'}});
}
=head2 _add_prediction
Title : _add_prediction()
Usage : $obj->_add_prediction($feat)
Function: internal
Example :
Returns :
=cut
sub _add_prediction {
my ($self, $gene) = @_;
if(! exists($self->{'_feats'})) {
$self->{'_feats'} = [];
}
push(@{$self->{'_feats'}}, $gene);
}
=head2 _predictions_parsed
Title : _predictions_parsed
Usage : $obj->_predictions_parsed
Function: internal
Example :
Returns : TRUE or FALSE
=cut
sub _predictions_parsed {
my ($self, $val) = @_;
$self->{'_preds_parsed'} = $val if $val;
if(! exists($self->{'_preds_parsed'})) {
$self->{'_preds_parsed'} = 0;
}
return $self->{'_preds_parsed'};
}
=head2 create_feature
Title : create_feature
Usage : obj->create_feature(\%feature)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub create_feature {
my ($self, $feat) = @_;
# create feature object
my $feature = Bio::SeqFeature::Generic->new(-seq_id => $feat->{name},
-start => $feat->{start},
-end => $feat->{end},
-score => $feat->{score},
-source => $feat->{source},
-primary => $feat->{primary},
-logic_name => $feat->{logic_name},
);
$feature->add_tag_value('evalue',0);
$feature->add_tag_value('percent_id','NULL');
$feature->add_tag_value("hid",$feat->{primary});
return $feature;
}
=head2 _read_fasta
Title : _read_fasta
Usage : obj->_read_fasta($file)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub _read_fasta {
local (*FILE) = @_;
my( $id , $seq , %name2seq);#bala
while (<FILE>) {
chomp;#bala
if (/^>(\S+)/) {
my $new_id = $1;
if ($id) {
$name2seq{$id} = $seq;
}
$id = $new_id ; $seq = "" ;
}
elsif (eof) {
if ($id) {
$seq .= $_ ;#bala line instead of $_
$name2seq{$id} = $seq;
}
}
else {
$seq .= $_
}
}
return %name2seq;
}
1;
]]>