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Bio::Tools::ESTScan(3)User Contributed Perl DocumentatioBio::Tools::ESTScan(3)

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

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 v5.24.1			  2017-07-08		Bio::Tools::ESTScan(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Hilmar Lapp | APPENDIX

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