Raw content of Bio::Tools::Signalp
<![CDATA[# Parser module for SignalP Bio::Tools::Signalp
#
# Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp
# 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::SignalP
=head1 SYNOPSIS
use Bio::Tools::SignalP;
my $parser = new Bio::Tools::SignalP(-fh =>$filehandle );
while( my $sp_feat = $parser->next_result ) {
#do something
#eg
push @sp_feat, $sp_feat;
}
=head1 DESCRIPTION
Parser for SignalP 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::Signalp
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::Signalp;
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 );
=head2 new
Title : new
Usage : my $obj = new Bio::Tools::SignalP();
Function: Builds a new Bio::Tools::SignalP object
Returns : Bio::Tools::SignalP
Args : -fh/-file => $val, # for initing input, see Bio::Root::IO
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self;
}
=head2 next_result
Title : next_result
Usage : my $feat = $signalp->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
=cut
sub next_result {
my ($self) = @_;
my $line;
# parse
my $id;
my ( $fact1, $fact2, $end);
while ($_=$self->_readline()) {
$line = $_;
chomp $line;
if ($line=~/^\>(\S+)/) {
$id = $1;
$self->seqname($id);
next;
}
elsif ($line=~/max\.\s+Y\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
$fact1 = $2;
$self->fact1($fact1);
next;
}
elsif ($line=~/mean\s+S\s+(\S+)\s+\S+\s+\S+\s+(\S+)/) {
$fact2 = $2;
$fact1 = $self->fact1;
$id = $self->seqname;
if ($fact1 eq "YES" && $fact2 eq "YES") {
my $line = $self->_readline();
if ($line =~ /Most likely cleavage site between pos\.\s+(\d+)/) {
$end = $1;
}
else {
$self->throw ("parsing problem in signalp");
}
my (%feature);
$feature{name} = $id;
$feature{start} = 1;
$feature{end} = $end;
$feature{source} = 'Signalp';
$feature{primary}= 'signal_peptide';
$feature{program} = 'Signalp';
$feature{logic_name} = 'signal_peptide';
my $new_feat = $self->create_feature (\%feature);
return $new_feat;
}
next;
}
next;
}
}
=head2 create_feature
Title : create_feature
Usage : obj->create_feature(\%feature)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub create_feature {
my ($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 $feature;
}
=head2 seqname
Title : seqname
Usage : obj->seqname($name)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub seqname{
my ($self,$seqname)=@_;
if (defined$seqname){
$self->{'seqname'}=$seqname;
}
return $self->{'seqname'};
}
=head2 fact1
Title : fact1
Usage : obj->fact1($fact1)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub fact1{
my ($self,$fact1)=@_;
if (defined$fact1){
$self->{'fact1'}=$fact1;
}
return $self->{'fact1'};
}
1;
]]>