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.

Mailing Lists
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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 email or the web: bioperl-bugs@bio.perl.org http://bugzilla.bioperl.org/ Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com) Describe contact details here 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 :