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Bio::Tools::Signalp::ExtendedSignalp.3pm

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 compability 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:

   http://bugzilla.open-bio.org/
 
 

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    :