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Bio::AlignIO::selex.3pm

NAME

Bio::AlignIO::selex - selex sequence input/output stream

SYNOPSIS

   # Do not use this module directly.  Use it via the L<Bio::AlignIO> class.
 
   use Bio::AlignIO;
   use strict;
 
   my $in = Bio::AlignIO->new(-format => 'selex',
                              -file   => 't/data/testaln.selex');
   while( my $aln = $in->next_aln ) {
 
   }
 
 

DESCRIPTION

This object can transform Bio::Align::AlignI objects to and from selex flat file databases.

FEEDBACK

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 the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu

CONTRIBUTORS

Jason Stajich, jason-at-bioperl.org

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

next_aln

  Title   : next_aln
  Usage   : $aln = $stream->next_aln()
  Function: returns the next alignment in the stream. Tries to read *all* selex
           It reads all non whitespace characters in the alignment
           area. For selexs with weird gaps (eg ~~~) map them by using
           $al->map_chars('~','-')
  Returns : L<Bio::Align::AlignI> object
  Args    : NONE
 
 

write_aln

  Title   : write_aln
  Usage   : $stream->write_aln(@aln)
  Function: writes the $aln object into the stream in selex format
  Returns : 1 for success and 0 for error
  Args    : L<Bio::Align::AlignI> object