GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
Bio::AlignIO::meme(3) User Contributed Perl Documentation Bio::AlignIO::meme(3)
 

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:
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.

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: 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 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
2019-01-01 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.