/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Signalp

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