Bio::Tools::Seg.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

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\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.

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:
   http://bugzilla.open-bio.org/
 
 

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