Bio::AlignIO::selex - selex sequence input/output stream
# 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 ) {
}
This object can transform Bio::Align::AlignI objects to and from selex flat file
databases.
Please direct usage questions or support issues to the mailing list:
[email protected]
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.
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://github.com/bioperl/bioperl-live/issues
Email:
[email protected]
Jason Stajich, jason-at-bioperl.org
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
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
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