Bio::Matrix::PSM::PsmHeaderI use Bio::Matrix::PSM::IO; #Obtain an Bio::Matrix::PSM::IO object: my $psmIO= new Bio::Matrix::PSM::IO(-file=>$file, -format=>'mast'); #Get some general data about the file you are parsing: my $release=$psmIO->release; my $version=$psmIO->version; print "This analysis was performed using MAST version $version, release $release\n"; #Now let's see what are the consensus sequences of the motifs fed as an input: my %seq=$psmIO->seq; #let's cycle through all consensus sequences now: foreach my $id ($psmIO->hid) { print "Motif $id is \t",$seq{$id},"\n"; } #Finally look at the stuff we do not parse: my @inputfile=grep(/datafile/i,$psmIO->unstructured); Generally you should not use this object directly, you can access the information through a PSM driver (See Bio::Matrix::PSM::IO). It is handling the header data from a PSM file which may be very different. This means that some of the methods will return undef naturally, because this information is not present in the file which is parsed. Some important data might be left over in the unstructured part, and you might have to parse it yourself. I will try to 'structure' this header more in the near future.

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new
Title : new Usage : my $header= new Bio::Matrix::PSM::PsmHeader ( -seq=>\%seq, -mid=>\%mid, -width=>\%width, -instances=>\%instances, -header=>\@header, -type=>'mast'); Function: Creates a new Bio::Matrix::PSM::PsmHeader object Throws : Example : Returns : Bio::Matrix::PSM::PsmHeader object Args : hash

seq
Title : seq Usage : my %seq= $header->seq(); Function: Returns the sequence data as a hash, indexed by a sequence ID (motif id or accession number) In case the input data is a motif it would return the consenus seq for each of them (mast). Throws : Example : Returns : hash Args :

hid
Title : hid Usage : my @ids= $header->hid(); Function: Returns array with the motif/instance ids Throws : Example : Returns : array Args :

length
Title : length Usage : my %length= $header->length(); Function: Returns the length of the input sequence or motifs as a hash, indexed by a sequence ID (motif id or accession number) Throws : Example : Returns : hash Args :

instances
Title : instances Usage : my %instances= $header->length(); Function: Returns the instance, used as a hash, indexed by a sequence ID (motif id or accession number) Throws : Example : Returns : hash of Bio::Matrix::PSM::InstanceSite objects Args :

weights
Title : weights Usage : my %weights= $header->weights(); Function: Returns the weights of the input sequence as a hash, indexed by a sequence ID Throws : Example : Returns : hash Args :

unstuctured
Title : unstuctured Usage : my @unstructured= $header->unstuctured(); Function: Returns the unstructured data in the header as an array, one line per array element, all control symbols are removed with \W Throws : Example : Returns : array Args :

version
Title : version Usage : my $version= $header->version; Function: Returns the version of the file being parsed if such exists Throws : Example : Returns : string Args :

revision
Title : revision Usage : my $revision= $header->revision; Function: Returns the revision of the file being parsed if such exists Throws : Example : Returns : string Args :

_check
Title : _check Usage : if ($self->_check('weights') { #do something} else {return undef;} Function: Checks if the method called is aplicable to the file format Throws : Example : Returns : boolean Args : string