Bio::Matrix::PSM::IO(3pm) User Contributed Perl Documentation Bio::Matrix::PSM::IO(3pm)
NAME
Bio::Matrix::PSM::IO - PSM parser
SYNOPSIS
use Bio::Matrix::PSM::IO;
my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac');
my $release=$psmIO->release; #Using Bio::Matrix::PSM::PsmHeader methods
my $release=$psmIO->release;
while (my $psm=$psmIO->next_psm) {
my %psm_header=$psm->header;
my $ic=$psm_header{IC};
my $sites=$psm_header{sites};
my $width=$psm_header{width};
my $score=$psm_header{e_val};
my $IUPAC=$psm->IUPAC;
}
my $instances=$psm->instances;
foreach my $instance (@{$instances}) {
my $id=$instance->primary_id;
}
DESCRIPTION
This module allows you to read DNA position scoring matrices and/or their respective sequence matches from a file.
There are two header methods, one belonging to Bio::Matrix::PSM::IO::driver and the other to Bio::Matrix::PSM::Psm. They provide general
information about the file (driver) and for the current PSM result (Psm) respectively. Psm header method always returns the same thing, but
some values in the hash might be empty, depending on the file you are parsing. You will get undef in this case (no exceptions are thrown).
Please note that the file header data (commenatries, version, input data, configuration, etc.) might be obtained through
Bio::Matrix::PSM::PsmHeader methods. Some methods are driver specific (meme, transfac, etc.): meme: weight mast: seq, instances
If called when you parse a different file type you will get undef. For example:
my $psmIO= Bio::Matrix::PSM::IO->new(file=>$file, format=>'transfac');
my %seq=$psmIO->seq;
will return an empty hash. To see all methods and how to use them go to Bio::Matrix::PSM::PsmHeaderI.
See also Bio::Matrix::PSM::PsmI for details on using and manipulating the parsed data.
The only way to write PFM/PWM is through masta module (something like fasta for DNA matrices). You can see an example by reading
Bio::Matrix::PSM::IO::masta documentation.
See also
Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::IO::masta
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan Kirov
Email skirov@utk.edu
APPENDIX
new
Title : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme',
-file=>$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. See L<Bio::Matrix::PSM::IO::meme> and
L<Bio::Matrix::PSM::IO::transfac> for more details.
Example :
Returns : psm object, associated with a file with matrix file
Args : hash
fh
Title : fh
Usage : $obj->fh
Function: Get a filehandle type access to the matrix parser
Example : $fh = $obj->fh; # make a tied filehandle
$matrix = <$fh>; # read a matrix object
Returns : filehandle tied to Bio::Matrix::PSM::IO class
Args : none
_load_format_module
Title : _load_format_module
Usage : *INTERNAL Matrix::PSM::IO stuff*
Function: Loads up (like use) a module at run time on demand
_guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Returns : guessed format of filename (lower case)
Args : filename
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
_parseMatrix
Title : _parseMatrix
Usage :
Function: Parses the next site matrix information in the meme file
Throws :
Example : Internal stuff
Returns : hash as for constructing a SiteMatrix object (see SiteMatrixI)
Args : string
_parseInstance
Title : _parseInstance
Usage :
Function: Parses the next sites instances from the meme file
Throws :
Example : Internal stuff
Returns : Bio::Matrix::PSM::SiteMatrix object
Args : array references
_parse_coordinates
Title : _parse_coordinates
Usage :
Function:
Throws :
Example : Internal stuff
Returns :
Args :
header
Title : header
Usage : my %header=$psmIO->header;
Function: Returns the header for the PSM file, format specific
Throws :
Example :
Returns : Hash or a single string with driver specific information
Args : none
_make_matrix
Title : _make_matrix
Usage :
Function: makes a matrix from 4 array references (A C G T)
Throws :
Example :
Returns : SiteMatrix object
Args : array of references(A C G T)
perl v5.14.2 2012-03-02 Bio::Matrix::PSM::IO(3pm)