| Bio::Tools::ESTScan(3pm) | User Contributed Perl Documentation | Bio::Tools::ESTScan(3pm) |
Bio::Tools::ESTScan - Results of one ESTScan run
$estscan = Bio::Tools::ESTScan->new(-file => 'result.estscan');
# filehandle:
$estscan = Bio::Tools::ESTScan->new( -fh => \*INPUT );
# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $genscan->next_feature() is the same
while($gene = $estscan->next_prediction()) {
# $gene is an instance of Bio::Tools::Prediction::Gene
foreach my $orf ($gene->exons()) {
# $orf is an instance of Bio::Tools::Prediction::Exon
$cds_str = $orf->predicted_cds();
}
}
# essential if you gave a filename at initialization (otherwise the file
# will stay open)
$estscan->close();
The ESTScan module provides a parser for ESTScan coding region prediction output.
This module inherits off Bio::Tools::AnalysisResult and therefore implements the Bio::SeqAnalysisParserI interface. See Bio::SeqAnalysisParserI.
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
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.
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
Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com)
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Usage : $estscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/estscan/i.
Returns : String
Argument : n/a
Title : next_feature
Usage : while($orf = $estscan->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the ESTScan result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
Title : next_prediction
Usage : while($gene = $estscan->next_prediction()) {
# do something
}
Function: Returns the next gene structure prediction of the ESTScan result
file. Call this method repeatedly until FALSE is returned.
So far, this method DOES NOT work for reverse strand predictions,
even though the code looks like.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
Title : close
Usage : $result->close()
Function: Closes the file handle associated with this result file.
Inherited method, overridden.
Example :
Returns :
Args :
Title : _fasta_stream
Usage : $result->_fasta_stream()
Function: Gets/Sets the FASTA sequence IO stream for reading the contents of
the file associated with this MZEF result object.
If called for the first time, creates the stream from the filehandle
if necessary.
Example :
Returns :
Args :
| 2020-10-28 | perl v5.30.3 |