Bio::Tools::ESTScan(3pm) User Contributed Perl Documentation Bio::Tools::ESTScan(3pm)
NAME
Bio::Tools::ESTScan - Results of one ESTScan run
SYNOPSIS
$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();
DESCRIPTION
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.
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 - Hilmar Lapp
Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com)
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
analysis_method
Usage : $estscan->analysis_method();
Purpose : Inherited method. Overridden to ensure that the name matches
/estscan/i.
Returns : String
Argument : n/a
next_feature
Title : next_feature
Usage : while($orf = $estscan->next_feature()) {
# do something
}
Function: Returns the next gene structure prediction of the ESTScan result
file. Call this method repeatedly until FALSE is returned.
The returned object is actually a SeqFeatureI implementing object.
This method is required for classes implementing the
SeqAnalysisParserI interface, and is merely an alias for
next_prediction() at present.
Example :
Returns : A Bio::Tools::Prediction::Gene object.
Args :
next_prediction
Title : next_prediction
Usage : while($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 :
close
Title : close
Usage : $result->close()
Function: Closes the file handle associated with this result file.
Inherited method, overridden.
Example :
Returns :
Args :
_fasta_stream
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 :
perl v5.14.2 2012-03-02 Bio::Tools::ESTScan(3pm)