Raw content of Bio::Tools::Signalp # 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;