Bio::Matrix::PSM::IO::mast - 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, than to PSM themselves.
Section III should be parsed too, otherwise no real sequence is available, so we
supply 'NNNNN....' as a seq which is not right.
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The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'mast',
Function: Associates a file with the appropriate parser
Throws : Throws if the file passed is in HTML format or if
some criteria for the file
format are not met.
Returns : psm object, associated with a file with matrix file
Args : hash
return : "Bio::Matrix::PSM::$format"->new(@args);
Title : next_psm
Usage : my $psm=$psmIO->next_psm();
Function: Reads the next PSM from the input file, associated with this object
Throws : Throws if there ara format violations in the input file (checking is not
very strict with all drivers).
Returns : Bio::Matrix::PSM::Psm object
Args : none
Title : write_psm
Usage : #Get SiteMatrix object somehow (see Bio::Matrix::PSM::SiteMatrix)
#Create the stream
#Will warn if only PFM data is contained in $matrix, recalculate the PWM
#based on normal distribution (A=>0.25, C=>0.25, etc)
Function: writes pwm in mast format
Args : SiteMatrix object