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

   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 - 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.

   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