Bio::Tools Seg
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Summary
Bio::Tools::Seg - parse seg output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::Generic
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
newDescriptionCode
next_resultDescriptionCode
Methods description
newcode    nextTop
 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_resultcodeprevnextTop
 Title   : next_result
Usage : my $feat = $seg->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::Generic
Args : none
Methods code
newdescriptionprevnextTop
sub new {
	my($class,@args) = @_;
	my $self = $class->SUPER::new(@args);
	$self->_initialize_io(@args);
	return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
	my ($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
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
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 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
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Torsten SeemannTop
Email - torsten.seemann AT infotech.monash.edu.au
CONTRIBUTOR - 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 _