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Bio::Matrix::PSM::PsmHeader(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::PsmHeader(3pm) NAME
Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation SYNOPSIS
# See Bio::Matrix::PSM::IO for detailed documentation on how to use # PSM parsers DESCRIPTION
Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM sequence matches 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::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 @hid= $header->hid(); Function: Returns array with the motif 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->instances(); Function: Returns the info about the input data, contained in the header Throws : Example : Returns : hash Args : weight Title : weight Usage : my %weights= $header->weight(); 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 : release Title : release Usage : my $release= $header->release; Function: Returns the release of the file being parsed if such exists Throws : Example : Returns : string Args : _check Title : _check Usage : if ($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::PsmHeader(3pm)
motif reqired for hp-ux 11.11