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.

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://github.com/bioperl/bioperl-live/issues

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    :

 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)