SYNOPSIS

use Bio::Tools::Eponine;
use strict;
my $seq = "/data/seq.fa";
my $threshold = "0.999";
my @params = ( -seq => $seq,
-threshold => $threshold);
my $factory = Bio::Tools::Run::Eponine->new(@params);
# run eponine against fasta
my $r = $factory->run_eponine($seq);
my $parser = Bio::Tools::Eponine->new($r);
while (my $feat = $parser->next_prediction){
#$feat contains array of SeqFeature
foreach my $orf($feat) {
print $orf->seq_id. "\n";
}
}

DESCRIPTION

Parser for Eponine, a probabilistic transcription start site detector optimized for mammalian genomic sequence. This module inherits off Bio::Tools::AnalysisResult and therefore implements Bio::SeqAnalysisParserI (see Bio::Tools::AnalysisResult and Bio::SeqAnalysisParserI).

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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:

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

AUTHOR - Tania Oh

<gisoht-at-nus.edu.sg>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

analysis_method

 Usage     : $mzef->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /mzef/i.
 Returns   : String
 Argument  : n/a

next_feature

 Title   : next_feature
 Usage   : while($gene = $mzef->next_feature()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the MZEF result
           file. Call this method repeatedly until FALSE is returned.
           The returned object is actually a SeqFeatureI implementing object.
           This method is required for classes implementing the
           SeqAnalysisParserI interface, and is merely an alias for 
           next_prediction() at present.
           Note that with the present version of MZEF there will only be one
           object returned, because MZEF does not predict individual genes
           but just potential internal exons.
 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

next_prediction

 Title   : next_prediction
 Usage   : while($gene = $mzef->next_prediction()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the MZEF result
           file. Call this method repeatedly until FALSE is returned.
           Note that with the present version of MZEF there will only be one
           object returned, because MZEF does not predict individual genes
           but just potential internal exons.
 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

_parse_predictions

 Title   : _parse_predictions()
 Usage   : $obj->_parse_predictions()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns :

create_feature

    Title   :   create_feature
    Usage   :   obj->create_feature($feature)
    Function:   Returns an array of features
    Returns :   Returns an array of features
    Args    :   none

_prediction

 Title   : _prediction()
 Usage   : $gene = $obj->_prediction()
 Function: internal
 Example :
 Returns :

_predictions_parsed

 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE