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.

[email protected]                  - General discussion
https://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Hilmar Lapp

Email [email protected] (or [email protected])

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    :

cpanm BioPerl

perl -MCPAN -e shell
install BioPerl