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://github.com/bioperl/bioperl-live/issues
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