Bio::Tools::Eponine(3pm) User Contributed Perl Documentation Bio::Tools::Eponine(3pm)
NAME
Bio::Tools::Eponine - Results of one Eponine run
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. "
";
}
}
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.
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:
https://redmine.open-bio.org/projects/bioperl/
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
perl v5.14.2 2012-03-02 Bio::Tools::Eponine(3pm)