#--------------------------------------------------------- # $Id: PsmHeaderI.pm 16123 2009-09-17 12:57:27Z cjfields $ =head1 NAME Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file =head1 SYNOPSIS use Bio::Matrix::PSM::IO; #Obtain an Bio::Matrix::PSM::IO object: my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$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); =head1 DESCRIPTION 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. =head1 FEEDBACK =head2 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 =head2 Support Please direct usage questions or support issues to the mailing list: I 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. =head2 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/ =head1 AUTHOR - Stefan Kirov Email skirov@utk.edu =head1 APPENDIX =cut # Let the code begin... package Bio::Matrix::PSM::PsmHeaderI; use Bio::Matrix::PSM::InstanceSite; use Bio::Matrix::PSM::Psm; use Bio::Matrix::PSM::IO; use strict; use base qw(Bio::Matrix::PSM::PsmI); #Accessor methods, based on the driver @Bio::Matrix::PSM::PsmHeader::MASTHEADER=qw(html version release seq hid length instances unstructured); @Bio::Matrix::PSM::PsmHeader::MEMEHEADER=qw(html version release hid weight length unstructured); @Bio::Matrix::PSM::PsmHeader::TRANSFACHEADER=qw(unstructured version release); @Bio::Matrix::PSM::PsmHeader::ALLHEADER=qw(header release type version html release weight length hid seq instances unstructured); =head2 new Title : new Usage : my $header= Bio::Matrix::PSM::PsmHeader->new ( -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::PsmHeaderI object Args : hash =cut =head2 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 : =cut sub seq { my $self = shift; $self->throw_not_implemented(); } =head2 hid Title : hid Usage : my @ids= $header->hid(); Function: Returns array with the motif/instance ids Throws : Example : Returns : array Args : =cut sub hid { my $self = shift; $self->throw_not_implemented(); } =head2 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 : =cut sub length { my $self = shift; $self->throw_not_implemented(); } =head2 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 : =cut sub instances { my $self = shift; $self->throw_not_implemented(); } =head2 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 : =cut sub weights { my $self = shift; $self->throw_not_implemented(); } =head2 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 : =cut sub unstructured { my $self = shift; $self->throw_not_implemented(); } =head2 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 : =cut sub version { my $self = shift; $self->throw_not_implemented(); } =head2 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 : =cut sub revision { my $self = shift; $self->throw_not_implemented(); } =head2 _check Title : _check Usage : if ($self->_check('weights') { #do something} else {return 0;} Function: Checks if the method called is aplicable to the file format Throws : Example : Returns : boolean Args : string =cut sub _check { my $self = shift; $self->throw_not_implemented(); } 1;