| Bio::Tools::Eponine(3pm) | User Contributed Perl Documentation | Bio::Tools::Eponine(3pm) |
Bio::Tools::Eponine - Results of one Eponine run
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";
}
}
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).
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Please direct usage questions or support issues to the mailing list:
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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.
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Usage : $mzef->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/mzef/i.
Returns : String
Argument : n/a
Title : next_feature
Usage : while($gene = $mzef->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the MZEF result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Note that with the present version of MZEF there will only be one
object returned, because MZEF does not predict individual genes
but just potential internal exons.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
Title : next_prediction
Usage : while($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 :
Title : _parse_predictions()
Usage : $obj->_parse_predictions()
Function: Parses the prediction section. Automatically called by
next_prediction() if not yet done.
Example :
Returns :
Title : create_feature
Usage : obj->create_feature($feature)
Function: Returns an array of features
Returns : Returns an array of features
Args : none
Title : _prediction() Usage : $gene = $obj->_prediction() Function: internal Example : Returns :
Title : _predictions_parsed Usage : $obj->_predictions_parsed Function: internal Example : Returns : TRUE or FALSE
| 2021-08-15 | perl v5.32.1 |