| Bio::AlignIO::selex(3pm) | User Contributed Perl Documentation | Bio::AlignIO::selex(3pm) |
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:
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.
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: schattner@alum.mit.edu
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
| 2018-10-27 | perl v5.26.2 |