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Bio::AlignIO::meme(3) User Contributed Perl DocumentationBio::AlignIO::meme(3)

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

SYNOPSIS
       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
	 }

DESCRIPTION
       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.

FEEDBACK
   Support
       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.

   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:

	 https://github.com/bioperl/bioperl-live/issues

AUTHORS	- Benjamin Berman
	Bbased 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 with the score() set to the evalue of	the
		  motif.
	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

perl v5.32.1			  2019-12-07		 Bio::AlignIO::meme(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Benjamin Berman | APPENDIX

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