bio::tools::run::signalp(3pm) [debian man page]
Bio::Tools::Run::Signalp(3pm) User Contributed Perl Documentation Bio::Tools::Run::Signalp(3pm) NAME
Bio::Tools::Run::Signalp SYNOPSIS
Build a Signalp factory my $factory = Bio::Tools::Run::Signalp->new(); # Pass the factory a Bio::Seq object # @feats is an array of Bio::SeqFeature::Generic objects my @feats = $factory->run($seq); DESCRIPTION
wrapper module for Signalp 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
Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written by Marc Sohrmann (ms2@sanger.ac.uk) Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org> Contributions by David Vilanova (david.vilanova@urbanet.ch) Shawn Hoon (shawnh@fugu-sg.org) # Please direct questions and support issues to <bioperl-l@bioperl.org> # Cared for by the Fugu Informatics team (fuguteam@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::Signalp->new(); Function: creates a new Signalp factory Returns: Bio::Tools::Run::Signalp Args : predict_protein_features Title : predict_protein_features() Usage : DEPRECATED. Use $factory->run($seq) instead Function: Runs Signalp and creates an array of featrues Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI run Title : run() Usage : my $feats = $factory->run($seq) Function: Runs Signalp Returns : An array of Bio::SeqFeature::Generic 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 signalp Returns : An array of Bio::SeqFeature::Generic 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::Signalp(3pm)
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Bio::Tools::Signalp(3pm) User Contributed Perl Documentation Bio::Tools::Signalp(3pm) NAME
Bio::Tools::Signalp - parser for Signalp output SYNOPSIS
use Bio::Tools::Signalp; my $parser = Bio::Tools::Signalp->new(-fh =>$filehandle ); while( my $sp_feat = $parser->next_result ) { if ($sp_feat->score > 0.9) { push @likely_sigpep, $sp_feat; } } DESCRIPTION
"SignalP" predicts the presence and location of signal peptide cleavage sites in amino acid sequences. Bio::Tools::Signalp parses the output of "SignalP" to provide a Bio::SeqFeature::Generic object describing the signal peptide found, if any. It returns a variety of tags extracted from the NN and HMM analysis. Most importantly, the "score()" attribute contains the NN probability of this being a true signal peptide. 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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted va the web: https://redmine.open-bio.org/projects/bioperl/ AUTHOR
# Please direct questions and support issues to bioperl-l@bioperl.org Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written by Marc Sohrmann (ms2_AT_sanger.ac.uk). Written in BioPipe by Balamurugan Kumarasamy savikalpa_AT_fugu-sg.org. Cared for by the Fugu Informatics team (fuguteam_AT_fugu-sg.org) CONTRIBUTORS
Torsten Seemann - torsten.seemann AT infotech.monash.edu.au APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ new Title : new Usage : my $obj = Bio::Tools::Signalp->new(); Function: Builds a new Bio::Tools::Signalp object Returns : Bio::Tools::Signalp Args : -fh/-file => $val, # for initing input, see Bio::Root::IO next_result Title : next_result Usage : my $feat = $signalp->next_result Function: Get the next result set from parser data Returns : Bio::SeqFeature::Generic Args : none _parse_hmm_result Title : _parse_hmm_result Usage : $self->_parse_hmm_result(\%feature) Function: Internal (not to be used directly) Returns : hash of feature values Args : hash of more feature values _create_feature Title : _create_feature Usage : $self->create_feature(\%feature) Function: Internal (not to be used directly) Returns : hash of feature values Args : hash of more feature values _seqname Title : _seqname Usage : $self->_seqname($name) Function: Internal (not to be used directly) Returns : Args : _fact1 Title : _fact1 Usage : $self->fact1($fact1) Function: Internal (not to be used directly) Returns : Args : perl v5.14.2 2012-03-02 Bio::Tools::Signalp(3pm)