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Bio::Matrix::PSM::IO::meme.3pm

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