Provided by: libbio-perl-perl_1.6.901-2_all bug

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)