| Bio::Matrix::PSM::PsmHeader(3pm) | User Contributed Perl Documentation | Bio::Matrix::PSM::PsmHeader(3pm) |
Bio::Matrix::PSM::PsmHeader - PSM mast parser implementation
# See Bio::Matrix::PSM::IO for detailed documentation on how to use # PSM parsers
Parser for mast. This driver unlike meme or transfac for example is dedicated more to PSM sequence matches
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
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.
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
Email skirov@utk.edu
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
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 :
Title : hid Usage : my @hid= $header->hid(); Function: Returns array with the motif ids Throws : Example : Returns : array Args :
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 :
Title : instances Usage : my %instances= $header->instances(); Function: Returns the info about the input data, contained in the header Throws : Example : Returns : hash Args :
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 :
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 :
Title : version Usage : my $version= $header->version; Function: Returns the version of the file being parsed if such exists Throws : Example : Returns : string Args :
Title : release Usage : my $release= $header->release; Function: Returns the release of the file being parsed if such exists Throws : Example : Returns : string Args :
Title : _check
Usage : if ($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
| 2020-10-28 | perl v5.30.3 |