NAME

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

SYNOPSIS

# Do not use this module directly.  Use it via the L<FAST::Bio::AlignIO> class.

use FAST::Bio::AlignIO;
use strict;

my $in = FAST::Bio::AlignIO->new(-format => 'selex',
                           -file   => 't/data/testaln.selex');
while( my $aln = $in->next_aln ) {

}

DESCRIPTION

This object can transform FAST::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<FAST::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<FAST::Bio::Align::AlignI> object