bio::tools::run::seg(3pm) [debian man page]
Bio::Tools::Run::Seg(3pm) User Contributed Perl Documentation Bio::Tools::Run::Seg(3pm) NAME
Bio::Tools::Run::Seg - Object for identifying low complexity regions in a given protein seequence. SYNOPSIS
# Build a Seg factory # $paramfile is the full path to the seg binary file my @params = ('PROGRAM',$paramfile); my $factory = Bio::Tools::Run::Seg->new($param); # Pass the factory a Bio::Seq object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq); DESCRIPTION
Seg is a program which identifies low complexity regions in proteins. It was developed by Wootton and Federhen at NCBI. 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, or undef if $SEGDIR not in ENV Args : None new Title : new Usage : $rm->new(@params) Function: creates a new Seg factory Returns: Bio::Tools::Run::Seg Args : predict_protein_features Title : predict_protein_features() Usage : DEPRECATED Use $obj->run($seq) instead Function: Runs Seg and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI run Title : run Usage : $obj->run($seq) Function: Runs Seg and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI _input Title : _input Usage : obj->_input($seqFile) Function: Internal (not to be used directly) Returns : Args : _run Title : _run Usage : $obj->_run() Function: Internal (not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args : None _writeSeqFile Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal (not to be used directly) Returns : string - Fasta filename to which $seq was written Args : Bio::Seq object perl v5.12.3 2011-06-18 Bio::Tools::Run::Seg(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)