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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)

Check Out this Related 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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