debian man page for bio::alignio::selex

Bio::AlignIO::selex(3pm)				User Contributed Perl Documentation				  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:

	 https://redmine.open-bio.org/projects/bioperl/

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

perl v5.14.2							    2012-03-02						  Bio::AlignIO::selex(3pm)