Bio::T...ESTScan(3pm)

🎀 Bio::T...ESTScan 🎀

okay bestie, so this is a page from the User Contributed Perl Documentation section of the manual — it's the Bio::T...ESTScan(3pm) page and it's literally all about parsing one ESTScan run 💖

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✨ NAME ✨

Bio::Tools::ESTScan — Results of one ESTScan run 🦋

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🌸 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();

no cap, that close() is essential if you handed it a filename at init — otherwise the file stays open forever and it's giving leaked filehandle energy 😭

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💅 DESCRIPTION 💅

The ESTScan module is your parser for ESTScan coding region prediction output. periodt.

It inherits off Bio::Tools::AnalysisResult, which means it implements the Bio::SeqAnalysisParserI interface. go look at Bio::SeqAnalysisParserI for the deets. 👑

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🫶 FEEDBACK 🫶

📬 Mailing Lists

User feedback is, like, an integral part of the evolution of this and other Bioperl modules — fr fr. 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

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👑 AUTHOR - Hilmar Lapp 👑

Email hlapp@gmx.net (or hilmar.lapp@pharma.novartis.com)

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🌈 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    :

⚠️ bestie listen: next_prediction DOES NOT work for reverse strand predictions so far, even though the code looks like it does. do not be fooled by the aesthetic 💀

🔍 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    :

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and that's the whole page, bestie — slay 💅✨

This one's from perl v5.32.1, dated 2021-08-15, and it lives in the Bio::T...ESTScan(3pm) manpage. go forth and parse those coding regions, you icon 🎀🦋💖