Bio::Matrix::PSM::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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new
Title : new Usage : my $psmIO = new Bio::Matrix::PSM::IO(-format=>'meme', -file=>$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

_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