Bio::Matrix::PSM IO
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Bio::Matrix::PSM::IO - PSM parser
Package variables
No package variables defined.
  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; }
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
  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
No description
Methods description
newcode    nextTop
 Title   : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=>'meme',
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 :
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
; } 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;
sub _parseMatrix {
    my $self = shift;
sub _parseInstance {
    my $self = shift;
sub _parse_coordinates {
    my $self = shift;
sub header {
    my $self = shift;
sub _make_matrix {
    my $self = shift;
    my $self = shift;

General documentation
See alsoTop
Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::IO::masta
Mailing ListsTop
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Support Top
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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
AUTHOR - Stefan KirovTop