debian man page for bio::tools::seg

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)