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:

         https://redmine.open-bio.org/projects/bioperl/

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