NAME¶

Bio::AlignIO::meme - meme sequence input/output stream

SYNOPSIS¶

Do not use this module directly. Use it via the Bio::AlignIO class.

  use Bio::AlignIO;
  # read in an alignment from meme
  my $in = Bio::AlignIO->new(-format => 'meme',
                             -file   => 'meme.out');
  while( my $aln = $in->next_aln ) {
     # do something with the alignment
  }

DESCRIPTION¶

This object transforms the "sites sorted by position p-value" sections of a meme (text) output file into a series of Bio::SimpleAlign objects. Each SimpleAlign object contains Bio::LocatableSeq objects which represent the individual aligned sites as defined by the central portion of the "site" field in the meme file. The start and end coordinates are derived from the "Start" field. See Bio::SimpleAlign and Bio::LocatableSeq for more information.

This module can only parse MEME version 3 and 4. Previous versions have output formats that are more difficult to parse correctly. If the meme output file is not version 3.0 or greater we signal an error.

FEEDBACK¶

  https://github.com/bioperl/bioperl-live/issues

AUTHORS - Benjamin Berman¶

 Bbased on the Bio::SeqIO modules by Ewan Birney and others
 Email: benb@fruitfly.berkeley.edu

APPENDIX¶

The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore.

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream
 Returns : Bio::SimpleAlign object with the score() set to the evalue of the
           motif.
 Args    : NONE

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: Not implemented
 Returns : 1 for success and 0 for error
 Args    : Bio::SimpleAlign object