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.\" ========================================================================
.\"
.IX Title "Bio::Tools::ESTScan 3pm"
.TH Bio::Tools::ESTScan 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Tools::ESTScan \- Results of one ESTScan run
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&   $estscan = Bio::Tools::ESTScan\->new(\-file => \*(Aqresult.estscan\*(Aq);
\&   # filehandle:
\&   $estscan = Bio::Tools::ESTScan\->new( \-fh  => \e*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();
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
The ESTScan module provides a parser for ESTScan coding region prediction
output.
.PP
This module inherits off Bio::Tools::AnalysisResult and therefore
implements the Bio::SeqAnalysisParserI interface. 
See Bio::SeqAnalysisParserI.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Hilmar Lapp"
.IX Header "AUTHOR - Hilmar Lapp"
Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com)
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
.SS "analysis_method"
.IX Subsection "analysis_method"
.Vb 5
\& Usage     : $estscan\->analysis_method();
\& Purpose   : Inherited method. Overridden to ensure that the name matches
\&             /estscan/i.
\& Returns   : String
\& Argument  : n/a
.Ve
.SS "next_feature"
.IX Subsection "next_feature"
.Vb 6
\& Title   : next_feature
\& Usage   : while($orf = $estscan\->next_feature()) {
\&                  # do something
\&           }
\& Function: Returns the next gene structure prediction of the ESTScan result
\&           file. Call this method repeatedly until FALSE is returned.
\&
\&           The returned object is actually a SeqFeatureI implementing object.
\&           This method is required for classes implementing the
\&           SeqAnalysisParserI interface, and is merely an alias for 
\&           next_prediction() at present.
\&
\& Example :
\& Returns : A Bio::Tools::Prediction::Gene object.
\& Args    :
.Ve
.SS "next_prediction"
.IX Subsection "next_prediction"
.Vb 6
\& Title   : next_prediction
\& Usage   : while($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    :
.Ve
.SS "close"
.IX Subsection "close"
.Vb 7
\& Title   : close
\& Usage   : $result\->close()
\& Function: Closes the file handle associated with this result file.
\&           Inherited method, overridden.
\& Example :
\& Returns :
\& Args    :
.Ve
.SS "_fasta_stream"
.IX Subsection "_fasta_stream"
.Vb 4
\& 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    :
.Ve