# Wrapper module for SignalP Bio::Tools::Run::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>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
=head1 NAME
Bio::Tools::Run::Signalp
=head1 SYNOPSIS
Build a Signalp factory
my $factory = Bio::Tools::Run::Signalp->new();
# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);
=head1 DESCRIPTION
wrapper module for Signalp program
=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
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>
Contributions by David Vilanova (david.vilanova@urbanet.ch)
Shawn Hoon (shawnh@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::Signalp;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR
$PROGRAMNAME @SIGNALP_PARAMS %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Factory::ApplicationFactoryI;
use Bio::Tools::Signalp;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
@SIGNALP_PARAMS=qw(PROGRAM VERBOSE);
foreach my $attr ( @SIGNALP_PARAMS)
{ $OK_FIELD{$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 'signalp';
}
=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{SIGNALPDIR}) if $ENV{SIGNALPDIR};
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
return $self->$attr if $self->$attr;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 new
Title : new
Usage : my $factory= Bio::Tools::Run::Signalp->new();
Function: creates a new Signalp factory
Returns: Bio::Tools::Run::Signalp
Args :
=cut
sub new {
my ($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 $factory->run($seq) instead
Function: Runs Signalp 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 : my $feats = $factory->run($seq)
Function: Runs Signalp
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
=cut
sub run {
my ($self,$seq) = @_;
my @feats;
if (ref($seq) ) {
if (ref($seq) =~ /GLOB/) {
$self->throw("cannot use filehandle");
}
my $infile1 = $self->_writeSeqFile($seq);
$self->_input($infile1);
@feats = $self->_run();
unlink $infile1;
}
else {
my $in = Bio::SeqIO->new(-file => $seq, '-format' =>'fasta');
my $infile1;
while ( my $tmpseq = $in->next_seq() ) {
$infile1 = $self->_writeSeqFile($tmpseq);
}
$self->_input($infile1);
@feats = $self->_run();
}
return @feats;
}
=head2 _input
Title : _input
Usage : $factory->_input($seqFile)
Function: get/set for input file
Returns :
Args :
=cut
sub _input() {
my ($self,$infile1) = @_;
$self->{'input'} = $infile1 if(defined $infile1);
return $self->{'input'};
}
=head2 _run
Title : _run
Usage : $factory->_run()
Function: Makes a system call and runs signalp
Returns : An array of Bio::SeqFeature::Generic objects
Args :
=cut
sub _run {
my ($self)= @_;
my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
my $str =$self->executable." -t euk -trunc 50 ".$self->{'input'}." > ".$outfile;
my $status = system($str);
$self->throw( "Signalp call ($str) crashed: $? \n") unless $status==0;
my $filehandle;
if (ref ($outfile) !~ /GLOB/) {
open (SIGNALP, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
$filehandle = \*SIGNALP;
}
else {
$filehandle = $outfile;
}
my $signalp_parser = Bio::Tools::Signalp->new(-fh=>$filehandle);
my @signalp_feat;
while(my $signalp_feat = $signalp_parser->next_result){
push @signalp_feat, $signalp_feat;
}
$self->cleanup();
close($tfh1);
undef $tfh1;
unlink $outfile;
return @signalp_feat;
}
=head2 _writeSeqFile
Title : _writeSeqFile
Usage : $factory->_writeSeqFile($seq)
Function: Creates a file from the given seq object
Returns : A string(filename)
Args : Bio::PrimarySeqI
=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);
$in->close();
close($tfh);
undef $tfh;
return $inputfile;
}
1;