SYNOPSIS
# 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);
DESCRIPTION
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.
FEEDBACK
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Support
Please direct usage questions or support issues to the mailing list: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 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 the web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Bala
Email [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _program_name
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
program_dir
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
predict_genes()
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
run
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
_run
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An array of Bio::Tools::Prediction::Gene objects Args :
_set_input()
Title : _set_input Usage : obj->_set_input($matrixFile,$seqFile) Function: Internal(not to be used directly) Returns : Args :
_writeSeqFile()
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal(not to be used directly) Returns : Args :