| Bio::Matrix::PSM::IO(3pm) | User Contributed Perl Documentation | Bio::Matrix::PSM::IO(3pm) |
Bio::Matrix::PSM::IO - PSM parser
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 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.
Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI, Bio::Matrix::PSM::IO::masta
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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:
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Email skirov@utk.edu
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
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)
| 2018-10-27 | perl v5.26.2 |