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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)


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.


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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
 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    :
2021-08-15 perl v5.32.1