Bio::Matrix::PSM::IO::User(Contributed Perl DocumBio::Matrix::PSM::IO::mast(3)NAMEBio::Matrix::PSM::IO::mast - 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, than to PSM themselves.
TO DO
Section III should be parsed too, otherwise no real sequence is
available, so we supply 'NNNNN....' as a seq which is not right.
FEEDBACK
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User feedback is an integral part of the evolution of this and other
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bioperl-l@bioperl.org - General discussion
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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
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'mast',
-file=>$file);
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.
Example :
Returns : psm object, associated with a file with matrix file
Args : hash
return : "Bio::Matrix::PSM::$format"->new(@args);
next_psm
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).
Example :
Returns : Bio::Matrix::PSM::Psm object
Args : none
write_psm
Title : write_psm
Usage : #Get SiteMatrix object somehow (see Bio::Matrix::PSM::SiteMatrix)
my $matrix=$psmin->next_matrix;
#Create the stream
my $psmio=new(-file=>">psms.mast",-format=>'mast');
$psmio->write_psm($matrix);
#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
Throws :
Example :
Args : SiteMatrix object
Returns :
perl v5.14.1 2011-07-22 Bio::Matrix::PSM::IO::mast(3)
