Bio::AlignIO::meme - meme sequence input/output stream
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
}
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.
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.
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
Bbased on the Bio::SeqIO modules by Ewan Birney and others
Email: [email protected]
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