bio::tools::run::genscan(3pm) [debian man page]
Bio::Tools::Run::Genscan(3pm) User Contributed Perl Documentation Bio::Tools::Run::Genscan(3pm) NAME
Bio::Tools::Run::Genscan - Object for identifying genes in a given sequence given a matrix(for appropriate organisms). 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
Mailing Lists 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. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support 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. 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 savikalpa@fugu-sg.org 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 : perl v5.12.3 2011-06-18 Bio::Tools::Run::Genscan(3pm)
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Bio::Tools::Run::Genemark(3pm) User Contributed Perl Documentation Bio::Tools::Run::Genemark(3pm) NAME
Bio::Tools::Run::Genemark - Wrapper for local execution of the GeneMark family of programs. SYNOPSIS
# GeneMark.hmm (prokaryotic) my $factory = Bio::Tools::Run::Genemark->new('-program' => 'gmhmmp', '-m' => 'model.icm'); # Pass the factory Bio::Seq objects # returns a Bio::Tools::Genemark object my $genemark = $factory->run($seq); DESCRIPTION
Wrapper module for the GeneMark family of programs. Should work with all flavors of GeneMark.hmm at least, although only the prokaryotic version has been tested. General information about GeneMark is available at <http://exon.gatech.edu/GeneMark/>. Contact information for licensing inquiries is available at: <http://opal.biology.gatech.edu/GeneMark/contact.html> Note that GeneMark.hmm (prokaryotic at least) will only process the first sequence in a fasta file (if you run() more than one sequence at a time, only the first will be processed). FEEDBACK
Mailing Lists 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. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists Support 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. 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 - Mark Johnson Email: mjohnson-at-watson-dot-wustl-dot-edu 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: gets/sets the program name Returns: string Args : string program_dir Title : program_dir Usage : $factory->program_dir() Function: gets/sets the program dir Returns: string Args : string new Title : new Usage : $genemark->new(@params) Function: creates a new Genemark factory Returns: Bio::Tools::Run::Genemark Args : run Title : run Usage : $obj->run($seq_file) Function: Runs Genemark Returns : A Bio::Tools::Genemark object Args : An array of Bio::PrimarySeqI objects _run Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An instance of Bio::Tools::Genemark Args : file name, sequence identifier (optional) _write_seq_file Title : _write_seq_file Usage : obj->_write_seq_file($seq) or obj->_write_seq_file(@seq) Function: Internal(not to be used directly) Returns : Name of a temp file containing program output Args : One or more Bio::PrimarySeqI objects perl v5.12.3 2011-06-18 Bio::Tools::Run::Genemark(3pm)