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Bio::Matrix::PSM::IO::User(Contributed Perl DocumBio::Matrix::PSM::IO::meme(3)

NAME
       Bio::Matrix::PSM::IO::meme - PSM meme parser implementation

SYNOPSIS
       See Bio::Matrix::PSM::IO for detailed documentation on how to use PSM
       parsers

DESCRIPTION
       Parser for meme.

FEEDBACK
   Mailing Lists
       User feedback is an integral part of the evolution of this and other
       Bioperl modules. Send your comments and suggestions preferably
	to one of the Bioperl mailing lists.  Your participation is much
       appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   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:

	 http://bugzilla.open-bio.org/

AUTHOR - Stefan Kirov
       Email skirov@utk.edu

APPENDIX
   new
	Title	: new
	Usage	: my $psmIO =  Bio::Matrix::PSM::IO->new(-format=>'meme',
							-file=>$file);
	Function: Associates a file with the appropriate parser
	Throws	: Throws if the file passed is in HTML format or
		  if the MEME header cannot be found.
	Example :
	Args	: hash
	Returns : "Bio::Matrix::PSM::$format"->new(@args);

   _parse_coordinates
	Title	: _parse_coordinates
	Usage	:
	Function:
	Throws	:
	Example : Internal stuff
	Returns :
	Args	:

   header
	Title	: header
	Usage	:  my %header=$psmIO->header;
	Function:  Returns the header for the MEME file
	Throws	:
	Example : Fetching all the sequences included in the MEME analysis,
		  being parsed
		  my %header=$psmIO->header;
		   foreach my $seqid (@{$header{instances}}) {
		      my $seq=$db->get_Seq_by_acc($id);
		      #Do something with the sequence
		   }
		   where $db might be Bio::DB:GenBank object, see
	Returns : Hash with three keys: instances, weights and lengths, which
		  should be self-explenatory. Each value is an array
		  reference. Each array element corresponds to the same
		  element in the other two arrays. So $header{instances}->[$i]
		  will refer to the same sequence in the motif file as
		  $header{weights}->[$i] and $header{lengths}->[$i]
	Args	:  none
	Notes	:  OBSOLETE!

   next_psm
	Title	: next_psm
	Usage	: my $psm=$psmIO->next_psm();
	Function: Reads the next PSM from the input file, associated with this object
	Throws	: Throws if the format is inconsistent with the rules for MEME 3.0.4:
		   no SUMMARY Section present or some keywords are missing/altered.
	Example :
	Returns : Bio::Matrix::PSM::Psm object
	Args	: none

   _parseMatrix
	Title	: _parseMatrix
	Usage	:
	Function: Parses the next site matrix information in the meme file
	Throws	:
	Example :  Internal stuff
	Returns :  hash as for constructing a SiteMatrix object (see SiteMatrixI)
	Args	:  string

   _parse_logs
	Title	: _parse_logs
	Usage	:
	Function: Parses the next site matrix log values in the meme file
	Throws	:
	Example :  Internal stuff
	Returns :  array of array refs
	Args	:  string

   _parseInstance
	Title	: _parseInstance
	Usage	:
	Function:  Parses the next sites instances from the meme file
	Throws	:
	Example :  Internal stuff
	Returns :  Bio::Matrix::PSM::InstanceSite object
	Args	:  none

perl v5.14.1			  2011-07-22	 Bio::Matrix::PSM::IO::meme(3)
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