Bio::Tools::Seg - parse C<seg> output

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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Bio::Tools::Seg - parse seg output

SYNOPSIS

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  use Bio::Tools::Seg;
  my $parser = Bio::Tools::Seg->(-file => 'seg.fasta');
  while ( my $f = $parser->next_result ) {
    if ($f->score < 1.5) {
      print $f->location->to_FTstring, " is low complexity\n";
    }
  }

DESCRIPTION

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seg identifies low-complexity regions on a protein sequence. It is usually part of the WU-BLAST and InterProScan packages.

The Bio::Tools::Seg module will only parse the "fasta" output modes of seg, i.e. seg -l (low complexity regions only), seg -h (high complexity regions only), or seg -a (both low and high).

It creates a Bio::SeqFeature::Generic for each FASTA-like entry found in the input file. It is up to the user to appropriately filter these using the feature's score.

FEEDBACK

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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/wiki/Mailing_lists  - About the mailing lists

Support

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 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 the web:

  https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Torsten Seemann

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Email - torsten.seemann AT infotech.monash.edu.au

CONTRIBUTOR - Bala

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Email - savikalpa@fugu-sg.org

APPENDIX

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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::Tools::Seg->new();
 Function: Builds a new Bio::Tools::Seg object
 Returns : Bio::Tools::Seg
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

next_result

 Title   : next_result
 Usage   : my $feat = $seg->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none
BioPerl documentation Contained in the BioPerl distribution. 
#
# BioPerl module for Bio::Tools::Seg
#
# Copyright Balamurugan Kumarasamy
# Totally re-written, added docs and tests -- Torsten Seemann, Sep 2006
#
# Copyright 
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code


package Bio::Tools::Seg;
use strict;

use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root Bio::Root::IO);



sub new {
	my($class,@args) = @_;
	my $self = $class->SUPER::new(@args);
	$self->_initialize_io(@args);
	return $self;
}


sub next_result {
	my ($self) = @_;

	# For example in this line 
	# test_prot(214-226) complexity=2.26 (12/2.20/2.50)
	# $1 is test_prot  
	# $2 is 214 
	# $3 is 226 
	# $4 is 2.26

	while (my $line = $self->_readline) {
		if ($line =~ /^\>\s*?(\S+)?\s*?\((\d+)\-(\d+)\)\s*complexity=(\S+)/) {
			return Bio::SeqFeature::Generic->new(
				-seq_id     => $1,
				-start      => $2,
				-end        => $3,
				-score      => $4,
				-source_tag => 'Seg',
				-primary    => 'low_complexity'
			);
		}
	}
}


1;