Toolbar

Summary

Bio::Tools::Seg - parse seg output

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

Synopsis

  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

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.

Methods

Methods description

 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

 Title   : next_result
 Usage   : my $feat = $seg->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::Generic
 Args    : none

Methods code

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;

}

General documentation

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

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.

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/

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

Email - savikalpa@fugu-sg.org

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