Bio::Tools::Run Signalp
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Bio::Tools::Run::Signalp
Package variables
No package variables defined.
Included modules
Bio::Factory::ApplicationFactoryI
Bio::Root::IO
Bio::Root::Root
Bio::SeqIO
Bio::Tools::Run::WrapperBase
Bio::Tools::Signalp
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
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);
Description
  wrapper module for Signalp program
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
AUTOLOAD
No description
Code
newDescriptionCode
predict_protein_featuresDescriptionCode
runDescriptionCode
_input()
No description
Code
_runDescriptionCode
_writeSeqFileDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
newcodeprevnextTop
 Title   : new
Usage : my $factory= Bio::Tools::Run::Signalp->new();
Function: creates a new Signalp factory
Returns: Bio::Tools::Run::Signalp
Args :
predict_protein_featurescodeprevnextTop
 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
runcodeprevnextTop
 Title   :   run()
Usage : my $feats = $factory->run($seq)
Function: Runs Signalp
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
_runcodeprevnextTop
 Title   :   _run
Usage : $factory->_run()
Function: Makes a system call and runs signalp
Returns : An array of Bio::SeqFeature::Generic objects
Args :
_writeSeqFilecodeprevnextTop
 Title   :   _writeSeqFile
Usage : $factory->_writeSeqFile($seq)
Function: Creates a file from the given seq object
Returns : A string(filename)
Args : Bio::PrimarySeqI
Methods code
BEGINTop
BEGIN {
       @SIGNALP_PARAMS=qw(PROGRAM VERBOSE);
       foreach my $attr ( @SIGNALP_PARAMS)
                        { $OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
    return 'signalp';
}
program_dirdescriptionprevnextTop
sub program_dir {
    return Bio::Root::IO->catfile($ENV{SIGNALPDIR}) if $ENV{SIGNALPDIR};
}
AUTOLOADdescriptionprevnextTop
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};
}
newdescriptionprevnextTop
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 $self;
}
predict_protein_featuresdescriptionprevnextTop
sub predict_protein_features {
    return shift->run(@_);
}
rundescriptionprevnextTop
sub run {
    my ($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;
}
_input()descriptionprevnextTop
sub _input() {
     my ($self,$infile1) = @_;
     $self->{'input'} = $infile1 if(defined $infile1);
     return $self->{'input'};
}
_rundescriptionprevnextTop
sub _run {
     my ($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;
}
_writeSeqFiledescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
Reporting BugsTop
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/
AUTHORTop
 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)
APPENDIXTop
 The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
_inputTop
 Title   :   _input
Usage : $factory->_input($seqFile)
Function: get/set for input file
Returns :
Args :