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)