Bio::Tools::RepeatMasker.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::RepeatMasker - a parser for RepeatMasker output

SYNOPSIS

     use Bio::Tools::RepeatMasker;
     my $parser = Bio::Tools::RepeatMasker->new(-file => 'seq.fa.out');
     while( my $result = $parser->next_result ) {
       # get some value
     }
 
 

DESCRIPTION

A parser for RepeatMasker output

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 - Shawn Hoon

Email shawnh@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::RepeatMasker->new();
  Function: Builds a new Bio::Tools::RepeatMasker object
  Returns : Bio::Tools::RepeatMasker
  Args    : -fh/-file => $val, for initing input, see Bio::Root::IO
 
 

next_result

  Title   : next_result
  Usage   : my $r = $rpt_masker->next_result
  Function: Get the next result set from parser data
  Returns : Bio::SeqFeature::FeaturePair
            Feature1 is the Query coordinates and Feature2 is the Hit
  Args    : none