Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a matrix(for appropriate organisms).
# Build a Genscan factory
my $param = ('MATRIX'=>HumanIso.smat);
my $factory = Bio::Tools::Run::Genscan->new($param);
# Pass the factory a Bio::Seq object
#@genes is an array of Bio::Tools::Predictions::Gene objects
my @genes = $factory->run($seq);
Genscan is a gene identifying program developed by Christopher Burge http://genes.mit.edu/burgelab/
By default it looks for an executable called genscan and data/parameter files in the directory specified by the GENSCANDIR environmental variable.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtiained from ENV variable. Returns: string Args :
Title : predict_genes()
Usage : DEPRECATED: use $obj->run($seq) instead
Function: Runs genscan and creates an array of Genes
Returns : An array of Bio::Tools::Prediction::Gene objects
Args : A Bio::PrimarySeqI
Title : run
Usage : $obj->run($seq)
Function: Runs genscan and creates an array of Genes
Returns : An array of Bio::Tools::Prediction::Gene objects
Args : A Bio::PrimarySeqI
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An array of Bio::Tools::Prediction::Gene objects
Args :
Title : _set_input
Usage : obj->_set_input($matrixFile,$seqFile)
Function: Internal(not to be used directly)
Returns :
Args :
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns :
Args :
