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

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq