| 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
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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
| 2018-10-27 | perl v5.26.2 |