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Bio::Tools::Signalp::EUserdContributed)Bio::Tools::Signalp::ExtendedSignalp(3)

NAME
       Bio::Tools::Signalp::ExtendedSignalp - enhanced parser for Signalp
       output

SYNOPSIS
	use Bio::Tools::Signalp::ExtendedSignalp;
	my $params = [qw(maxC maxY maxS	meanS D)];
	my $parser = new Bio::Tools::Signalp::ExtendedSignalp(
							      -fh      => $filehandle
							      -factors => $params
							     );

	$parser->factors($params);
	while( my $sp_feat = $parser->next_feature ) {
	      #do something
	      #eg
	      push @sp_feat, $sp_feat;
	}

DESCRIPTION
       # Please	direct questions and support issues to bioperl-l@bioperl.org

       Parser module for Signalp.

       Based on	the EnsEMBL module
       Bio::EnsEMBL::Pipeline::Runnable::Protein::Signalp originally written
       by Marc Sohrmann	(ms2 a sanger.ac.uk) Written in	BioPipe	by Balamurugan
       Kumarasamy (savikalpa a fugu-sg.org) Cared for by the Fugu Informatics
       team (fuguteam@fugu-sg.org)

       You may distribute this module under the	same terms as perl itself

       Compared	to the original	SignalP, this method allow the user to filter
       results out based on maxC maxY maxS meanS and D factor cutoff for the
       Neural Network (NN) method only.	The HMM	method does not	give any
       filters with 'YES' or 'NO' as result.

       The user	must be	aware that the filters can only	by applied on NN
       method.	Also, to ensure	the compatibility with original	Signalp
       parsing module, the user	must know that by default, if filters are
       empty, max Y and	mean S filters are automatically used to filter
       results.

       If the used gives a list, then the parser will only report protein
       having 'YES' for	each factor.

       This module supports parsing for	full, summary and short	output form
       signalp.	 Actually, full	and summary are	equivalent in terms of
       filtering results.

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 via the
       web:

	 https://github.com/bioperl/bioperl-live/issues

AUTHOR
	Based on the Bio::Tools::Signalp module
	Emmanuel Quevillon <emmanuel.quevillon@versailles.inra.fr>

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 = new	Bio::Tools::Signalp::ExtendedSignalp();
	Function: Builds a new Bio::Tools::Signalp::ExtendedSignalp object
	Returns	: Bio::Tools::Signalp::ExtendedSignalp
	Args	: -fh/-file => $val, # for initing input, see Bio::Root::IO

   next_feature
	Title	: next_feature
	Usage	: my $feat = $signalp->next_feature
	Function: Get the next result feature from parser data
	Returns	: Bio::SeqFeature::Generic
	Args	: none

   _filterok
	Title	: _filterok
	Usage	: my $feat = $signalp->_filterok
	Function: Check	if the factors required	by the user are	all ok.
	Returns	: 1/0
	Args	: hash reference

   factors
	Title	: factors
	Usage	: my $feat = $signalp->factors
	Function: Get/Set the filters required from the	user
	Returns	: hash
	Args	: array	reference

   _parsed
	Title	: _parsed
	Usage	: obj->_parsed()
	Function: Get/Set if the result	is parsed or not
	Returns	: 1/0 scalar
	Args	: On set 1

   _parse
	Title	: _parse
	Usage	: obj->_parse
	Function: Parse	the SignalP result
	Returns	:
	Args	:

   _parse_summary_format
	Title	: _parse_summary_format
	Usage	: $self->_parse_summary_format
	Function: Method to parse summary/full format from signalp output
		  It automatically fills filtered features.
	Returns	:
	Args	:

   _parse_nn_result
	Title	: _parse_nn_result
	Usage	: obj->_parse_nn_result
	Function: Parses the Neuronal Network (NN) part	of the result
	Returns	: Hash reference
	Args	:

   _parse_hmm_result
	Title	: _parse_hmm_result
	Usage	: obj->_parse_hmm_result
	Function: Parses the Hiden Markov Model	(HMM) part of the result
	Returns	: Hash reference
	Args	:

   _parse_short_format
	Title	: _parse_short_format
	Usage	: $self->_parse_short_format
	Function: Method to parse short	format from signalp output
		  It automatically fills filtered features.
	Returns	:
	Args	:

   create_feature
	Title	: create_feature
	Usage	: obj->create_feature(\%feature)
	Function: Internal(not to be used directly)
	Returns	:
	Args	:

   seqname
	Title	: seqname
	Usage	: obj->seqname($name)
	Function: Internal(not to be used directly)
	Returns	:
	Args	:

perl v5.32.1			  2019-Bio::Tools::Signalp::ExtendedSignalp(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX

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