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motif reqired for hp-ux 11.11
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Bio::Matrix::PSM::PsmHeaderI(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::PsmHeaderI(3pm) NAME
Bio::Matrix::PSM::PsmHeaderI - handles the header data from a PSM file 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 $release "; #Now let's see what are the consensus sequences of the motifs fed as an input: my %seq=$psmIO->seq; #let's cycle through all consensus sequences now: foreach my $id ($psmIO->hid) { print "Motif $id is ",$seq{$id}," "; } #Finally look at the stuff we do not parse: my @inputfile=grep(/datafile/i,$psmIO->unstructured); 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. 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: https://redmine.open-bio.org/projects/bioperl/ AUTHOR - Stefan Kirov Email skirov@utk.edu APPENDIX
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 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 0;} Function: Checks if the method called is aplicable to the file format Throws : Example : Returns : boolean Args : string perl v5.14.2 2012-03-02 Bio::Matrix::PSM::PsmHeaderI(3pm)
motif reqired for hp-ux 11.11