Bio::Tools::Run::Signalp 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); wrapper module for Signalp program

Mailing Lists
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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://bugzilla.bioperl.org/ 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) Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org) 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, obtiained 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