Bio::Matrix::PSM IO
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Matrix::PSM::IO - PSM parser
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
strict
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
  use Bio::Matrix::PSM::IO;

  my $psmIO= new Bio::Matrix::PSM::IO(-file=>$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 $psmIO= new Bio::Matrix::PSM::IO(file=>$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.
Methods
newDescriptionCode
fhDescriptionCode
_load_format_moduleDescriptionCode
_guess_formatDescriptionCode
next_psmDescriptionCode
_parseMatrixDescriptionCode
_parseInstanceDescriptionCode
_parse_coordinatesDescriptionCode
headerDescriptionCode
_make_matrixDescriptionCode
DESTROY
No description
Code
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $psmIO =  new Bio::Matrix::PSM::IO(-format=>'meme', 
						 -file=>$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
fhcodeprevnextTop
 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_modulecodeprevnextTop
 Title   : _load_format_module
 Usage   : *INTERNAL Matrix::PSM::IO stuff*
 Function: Loads up (like use) a module at run time on demand
_guess_formatcodeprevnextTop
 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Returns : guessed format of filename (lower case)
 Args    : filename
next_psmcodeprevnextTop
 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
_parseMatrixcodeprevnextTop
 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
_parseInstancecodeprevnextTop
 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_coordinatescodeprevnextTop
 Title   : _parse_coordinates
 Usage   :
 Function:
 Throws  :
 Example : Internal stuff
 Returns :
 Args    :
headercodeprevnextTop
 Title   : header
 Usage   :  my %header=$psmIO->header;
 Function:  Returns the header for the PSM file, format specific
 Throws  :
 Example :
 Returns :  Hash or a single string with driver specific information
 Args    :  none
_make_matrixcodeprevnextTop
 Title   : _make_matrix
 Usage   :
 Function: makes a matrix from 4 array references (A C G T)
 Throws  :
 Example :
 Returns : SiteMatrix object
 Args    : array of references(A C G T)
Methods code
newdescriptionprevnextTop
sub new {
    my($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'; $self->throw("$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 undef unless( $class->_load_format_module($format) ); return "Bio::Matrix::PSM::IO::$format"->new(@args); }
}
fhdescriptionprevnextTop
sub fh {
    my $self = shift;
    my $class = ref($self) || $self;
    my $s = Symbol::gensym;
    tie $$s,$class,$self;
    return $s;
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($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;
}
_guess_formatdescriptionprevnextTop
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;
}
next_psmdescriptionprevnextTop
sub next_psm {
    my $self = shift;
    $self->throw_not_implemented();
}
_parseMatrixdescriptionprevnextTop
sub _parseMatrix {
    my $self = shift;
    $self->throw_not_implemented();
}
_parseInstancedescriptionprevnextTop
sub _parseInstance {
    my $self = shift;
    $self->throw_not_implemented();
}
_parse_coordinatesdescriptionprevnextTop
sub _parse_coordinates {
    my $self = shift;
    $self->throw_not_implemented();
}
headerdescriptionprevnextTop
sub header {
    my $self = shift;
    $self->throw_not_implemented();
}
_make_matrixdescriptionprevnextTop
sub _make_matrix {
    my $self = shift;
    $self->throw_not_implemented();
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;
    $self->close();
}
General documentation
See alsoTop
Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI
FEEDBACKTop
Mailing ListsTop
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://bio.perl.org/MailList.html     - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
APPENDIXTop