Bio::Tools::Run Seg
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Summary
Bio::Tools::Run::Seg - Object for identifying low complexity
regions in a given protein seequence.
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
Bio::SeqIO
Bio::Tools::Run::WrapperBase
Bio::Tools::Seg
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
Synopsis
  # Build a Seg factory
  # $paramfile is the full path to the seg binary file
  my @params = ('PROGRAM',$paramfile);
  my $factory = Bio::Tools::Run::Seg->new($param);

  # Pass the factory a Bio::Seq object
  # @feats is an array of Bio::SeqFeature::Generic objects
  my @feats = $factory->run($seq);
Description
Seg is a program which identifies low complexity regions in proteins.
It was developed by Wootton and Federhen at NCBI.
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
AUTOLOAD
No description
Code
newDescriptionCode
predict_protein_featuresDescriptionCode
runDescriptionCode
_inputDescriptionCode
_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, or undef if $SEGDIR not in ENV
 Args    : None
newcodeprevnextTop
 Title   : new
 Usage   : $rm->new(@params)
 Function: creates a new Seg factory
 Returns:  Bio::Tools::Run::Seg
 Args    :
predict_protein_featurescodeprevnextTop
 Title   :   predict_protein_features()
 Usage   :   DEPRECATED Use $obj->run($seq) instead
 Function:   Runs Seg and creates an array of featrues
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI
runcodeprevnextTop
 Title   :   run
 Usage   :   $obj->run($seq)
 Function:   Runs Seg and creates an array of featrues
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   A Bio::PrimarySeqI
_inputcodeprevnextTop
 Title   :   _input
 Usage   :   obj->_input($seqFile)
 Function:   Internal (not to be used directly)
 Returns :
 Args    :
_runcodeprevnextTop
 Title   :   _run
 Usage   :   $obj->_run()
 Function:   Internal (not to be used directly)
 Returns :   An array of Bio::SeqFeature::Generic objects
 Args    :   None
_writeSeqFilecodeprevnextTop
 Title   :   _writeSeqFile
 Usage   :   obj->_writeSeqFile($seq)
 Function:   Internal (not to be used directly)
 Returns :   string - Fasta filename to which $seq was written
 Args    :   Bio::Seq object
Methods code
BEGINTop
BEGIN {
       @SEG_PARAMS=qw(PROGRAM VERBOSE);
       foreach my $attr ( @SEG_PARAMS)
                        { $OK_FIELD{$attr}++;
}
program_namedescriptionprevnextTop
sub program_name {
        return 'seg';
}
program_dirdescriptionprevnextTop
sub program_dir {
        return Bio::Root::IO->catfile($ENV{SEGDIR}) if $ENV{SEGDIR};
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
       my $self = shift;
       my $attr = $AUTOLOAD;
       $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 =~ /^-/ );
           $self->$attr($value);
       }
       return $self;
}
predict_protein_featuresdescriptionprevnextTop
sub predict_protein_features {
	return shift->run(@_);
}
rundescriptionprevnextTop
sub run {
    my ($self,$seq) = @_;
    my @feats;

    if (ref($seq) ) { # it is an object
        if (ref($seq) =~ /GLOB/) {
            $self->throw("cannot use filehandle");
        }

        my $infile1 = $self->_writeSeqFile($seq);

        $self->_input($infile1);

        @feats = $self->_run();
        unlink $infile1;
    }
    else {
        #The seq object is not a seq object but a file.
        #Here the file does not need to be created.

        $self->_input($seq);

        @feats = $self->_run();

    }

    return @feats;
}
_inputdescriptionprevnextTop
sub _input {
     my ($self,$infile1) = @_;
     if(defined $infile1){

         $self->{'input'}=$infile1;
     }
     return $self->{'input'};
}
_rundescriptionprevnextTop
sub _run {
     my ($self)= @_;

     my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
     my $str =$self->executable." ".$self->_input." -l > ".$outfile;
     my $status = system($str);
     $self->throw( "Seg call ($str) crashed: $?\n ") unless $status==0;
     
     my $filehandle;
     if (ref ($outfile) !~ /GLOB/) {
        open (SEG, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
        $filehandle =\* SEG;
     }
     else {
        $filehandle = $outfile;
     }
     my $seg_parser = Bio::Tools::Seg->new(-fh=>$filehandle);

     my @seg_feat;

     while(my $seg_feat = $seg_parser->next_result){

          push @seg_feat, $seg_feat;
     }
     # free resources
     $self->cleanup();
     unlink $outfile;
     close($tfh1);
     undef $tfh1;
     return @seg_feat;
}
_writeSeqFiledescriptionprevnextTop
sub _writeSeqFile {
    my ($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/
AUTHOR - BalaTop
 Email savikalpa@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _