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Summary

Bio::Matrix::PSM::IO - PSM parser

Package variables

Inherit

Bio::Root::IO

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.

Methods

Methods description

 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 Bio::Matrix::PSM::IO::meme and 
           Bio::Matrix::PSM::IO::transfac for more details.
 Example :
 Returns : psm object, associated with a file with matrix file
 Args    : hash

 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

 Title   : _load_format_module
 Usage   : *INTERNAL Matrix::PSM::IO stuff*
 Function: Loads up (like use) a module at run time on demand

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Returns : guessed format of filename (lower case)
 Args    : filename

 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

 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

 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

 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

 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)

Methods code

sub new {

    my($caller,@args) = @_;
    my $class = ref($caller) || $caller;
    my $self;
    # or do we want to call SUPER on an object if $caller is an
    # object?
    if( $class =~ /Bio::Matrix::PSM::IO(\S+)/ ) {
	$self = $class->SUPER::new(@args);
	$self->_initialize(@args);
	return $self;
    } else {
	my %param = @args;
	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
	my $format = $param{'-format'} ||
	    $class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
	    'scoring';
	$class->throw("$format format unrecognized or an argument error occured\n.") if (!grep(/$format/,@Bio::Matrix::PSM::IO::PSMFORMATS));
	$format = "\L$format"; # normalize capitalization to lower case

	# normalize capitalization
	return unless( $class->_load_format_module($format) );
	return "Bio::Matrix::PSM::IO::$format"->new(@args);
    }

}

sub fh {

    my $self = shift;
    my $class = ref($self) || $self;
    my $s = Symbol::gensym;
    tie $$s,$class,$self;
    return $s;

}

sub _load_format_module {

  my ($self,$format) = @_;
  my $module = "Bio::Matrix::PSM::IO::" . $format;
  my $ok;

  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the Matrix::PSM::IO system please see the
Matrix::PSM::IO docs.  This includes ways of checking for formats at
compile time, not run time
END
  ;
  }
  return $ok;

}

sub _guess_format {

    my $class = shift;
    return unless $_ = shift;
    return 'meme'   if /.meme$|meme.html$/i;
    return 'transfac'   if /\.dat$/i;
    return 'mast'   if /^mast\.|\.mast.html$|.mast$/i;

}

sub next_psm {

    my $self = shift;
    $self->throw_not_implemented();

}

sub _parseMatrix {

    my $self = shift;
    $self->throw_not_implemented();

}

sub _parseInstance {

    my $self = shift;
    $self->throw_not_implemented();

}

sub _parse_coordinates {

    my $self = shift;
    $self->throw_not_implemented();

}

sub header {

    my $self = shift;
    $self->throw_not_implemented();

}

sub _make_matrix {

    my $self = shift;
    $self->throw_not_implemented();

}

sub DESTROY {

    my $self = shift;
    $self->close();
}

1;

}

General documentation

Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::IO::masta

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.

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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.

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/

Email skirov@utk.edu