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)