Bio::Matrix::PSM::IO - PSM parser 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; } 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. Bio::Matrix::PSM::PsmI, Bio::Matrix::PSM::PsmHeaderI

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Reporting Bugs
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/ Email skirov@utk.edu

new
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 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

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

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

next_psm
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

_parseMatrix
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

_parseInstance
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_coordinates
Title : _parse_coordinates Usage : Function: Throws : Example : Internal stuff Returns : Args :

header
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_matrix
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)