Bio::Tools::Seg(3pm) User Contributed Perl Documentation Bio::Tools::Seg(3pm)
NAME
Bio::Tools::Seg - parse "seg" output
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
";
}
}
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.
FEEDBACK
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
Email - torsten.seemann AT infotech.monash.edu.au
CONTRIBUTOR - Bala
Email - savikalpa@fugu-sg.org
APPENDIX
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
perl v5.14.2 2012-03-02 Bio::Tools::Seg(3pm)