Bio::Matrix::PSM::PsmHUserrContributed Perl DocuBio::Matrix::PSM::PsmHeader(3)NAMEBio::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:
http://bugzilla.open-bio.org/
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 v5.14.1 2011-07-22 Bio::Matrix::PSM::PsmHeader(3)
