Bio::Matrix::PSM IO
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Summary
Bio::Matrix::PSM::IO - PSM parser
Package variables
No package variables defined.
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
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 $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme',
-file=>$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
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'; $class->throw("$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); }
}
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();
}

1;
}
General documentation
See alsoTop
Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::IO::masta
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support Top
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 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 the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Stefan KirovTop
Email skirov@utk.edu
APPENDIXTop