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.\"
.IX Title "Bio::AlignIO::meme 3pm"
.TH Bio::AlignIO::meme 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::AlignIO::meme \- meme sequence input/output stream
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
Do not use this module directly.  Use it via the Bio::AlignIO class.
.PP
.Vb 7
\&  use Bio::AlignIO;
\&  # read in an alignment from meme
\&  my $in = Bio::AlignIO\->new(\-format => \*(Aqmeme\*(Aq,
\&                             \-file   => \*(Aqmeme.out\*(Aq);
\&  while( my $aln = $in\->next_aln ) {
\&     # do something with the alignment
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This object transforms the \*(L"sites sorted by position p\-value\*(R" 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 \*(L"site\*(R" field in the meme file.  The start
and end coordinates are derived from the \*(L"Start\*(R" field. See
Bio::SimpleAlign and Bio::LocatableSeq for more information.
.PP
This module can only parse \s-1MEME\s0 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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHORS \- Benjamin Berman"
.IX Header "AUTHORS - Benjamin Berman"
.Vb 2
\& Bbased on the Bio::SeqIO modules by Ewan Birney and others
\& Email: benb@fruitfly.berkeley.edu
.Ve
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with an
underscore.
.SS "next_aln"
.IX Subsection "next_aln"
.Vb 6
\& 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
.Ve
.SS "write_aln"
.IX Subsection "write_aln"
.Vb 5
\& Title   : write_aln
\& Usage   : $stream\->write_aln(@aln)
\& Function: Not implemented
\& Returns : 1 for success and 0 for error
\& Args    : Bio::SimpleAlign object
.Ve