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 3.0 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.
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:
http://bugzilla.open-bio.org/
Bbased on the Bio::SeqIO modules by Ewan Birney and others Email: benb@fruitfly.berkeley.edu
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 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
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.