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.
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:
http://bugzilla.open-bio.org/
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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.