| Bio::Tools::Run::Genscan(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Genscan(3pm) |
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.
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.
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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.
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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, obtained 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 :
| 2023-01-22 | perl v5.36.0 |