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

Support

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.

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

AUTHORS - Benjamin Berman

 Bbased on the Bio::SeqIO modules by Ewan Birney and others
 Email: [email protected]

APPENDIX

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

next_aln

 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

write_aln

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