# Copyright Balamurugan Kumarasamy
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Seg - Object for identifying low complexity
regions in a given protein seequence.
=head1 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);
=head1 DESCRIPTION
Seg is a program which identifies low complexity regions in proteins.
It was developed by Wootton and Federhen at NCBI.
=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 - Bala
Email savikalpa@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::Seg;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR
$PROGRAMNAME @SEG_PARAMS %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Seg;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
@SEG_PARAMS=qw(PROGRAM VERBOSE);
foreach my $attr ( @SEG_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 'seg';
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string, or undef if $SEGDIR not in ENV
Args : None
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{SEGDIR}) if $ENV{SEGDIR};
}
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};
}
=head2 new
Title : new
Usage : $rm->new(@params)
Function: creates a new Seg factory
Returns: Bio::Tools::Run::Seg
Args :
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ );
$self->$attr($value);
}
return $self;
}
=head2 predict_protein_features
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
=cut
sub predict_protein_features{
return shift->run(@_);
}
=head2 run
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
=cut
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 = $self->_run();
}
return @feats;
}
=head2 _input
Title : _input
Usage : obj->_input($seqFile)
Function: Internal (not to be used directly)
Returns :
Args :
=cut
sub _input {
my ($self,$infile1) = @_;
if(defined $infile1){
$self->{'input'}=$infile1;
}
return $self->{'input'};
}
=head2 _run
Title : _run
Usage : $obj->_run()
Function: Internal (not to be used directly)
Returns : An array of Bio::SeqFeature::Generic objects
Args : None
=cut
sub _run {
my ($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 $tfh1;
return @seg_feat;
}
=head2 _writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal (not to be used directly)
Returns : string - Fasta filename to which $seq was written
Args : Bio::Seq object
=cut
sub _writeSeqFile{
my ($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;