Christopher Fields > BioPerl-1.6.901 > Bio::Matrix::PSM::IO::meme



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Module Version: 1.006901   Source   Latest Release: BioPerl-1.6.924


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


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


Parser for meme.


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AUTHOR - Stefan Kirov ^




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


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


 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!


 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


 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


 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


 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
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