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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:

   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