bio::tools::run::profile(3pm) [debian man page]
Bio::Tools::Run::Profile(3pm) User Contributed Perl Documentation Bio::Tools::Run::Profile(3pm) NAME
Bio::Tools::Run::Profile SYNOPSIS
Build a Profile factory # $paramfile is the full path to the seg binary file my @params = ('DB',$dbfile,'PROGRAM',$paramfile); my $factory = Bio::Tools::Run::Profile->new($param); # Pass the factory a Bio::PrimarySeqI object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq); DESCRIPTION
Wrapper module for the pfscan program 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 - Balamurugan Kumarasamy Email: fugui@worf.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 : new Title : new Usage : my $factory= Bio::Tools::Run::Profile->new($param); Function: creates a new Profile factory Returns: Bio::Tools::Run::Profile Args : predict_protein_features Title : predict_protein_features Usage : DEPRECATED. Use $factory->run($seq) instead. Function: Runs Profile and creates an array of featrues Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : A Bio::PrimarySeqI run Title : run Usage : my @feats = $factory->run($seq) Function: Runs Profile Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : A Bio::PrimarySeqI _input Title : _input Usage : $factory->_input($seqFile) Function: get/set for input file Returns : Args : _run Title : _run Usage : $factory->_run() Function: Makes a system call and runs pfscan Returns : An array of L<Bio::SeqFeature::FeaturePair> objects Args : _writeSeqFile Title : _writeSeqFile Usage : $factory->_writeSeqFile($seq) Function: Creates a file from the given seq object Returns : A string(filename) Args : Bio::PrimarySeqI perl v5.12.3 2011-06-18 Bio::Tools::Run::Profile(3pm)
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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)