Christopher Fields > BioPerl-1.6.901 > Bio::AlignIO::selex

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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924

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
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