Ewan Birney

NAME

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

SYNOPSIS

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

DESCRIPTION

This object transforms the "sites sorted by 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 3.0 and greater. 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

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 email or the web:

 bioperl-bugs@bio.perl.org
 http://bio.perl.org/bioperl-bugs/

AUTHORS - Benjamin Berman

 (based 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
 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