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

💖 Bio::Tools::Genemark 💖

okay bestie, so this is a page from the User Contributed Perl Documentation, and it's literally all about Bio::Tools::Genemark — the lil module that holds the results of one Genemark run. pull up a chair, we're doing bioinformatics and we're doing it cute 🧚✨

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🌸 NAME 🌸

Bio::Tools::Genemark — results of one Genemark run, bestie. that's it, that's the whole vibe 💅

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✨ SYNOPSIS ✨

okay so here's how you actually use this thing, no cap:

   $Genemark = Bio::Tools::Genemark->new(-file => 'result.Genemark');
   # filehandle:
   $Genemark = Bio::Tools::Genemark->new( -fh  => \*INPUT );

   # parse the results
   # note: this class is-a Bio::Tools::AnalysisResult which implements
   # Bio::SeqAnalysisParserI, i.e., $Genemark->next_feature() is the same
   while($gene = $Genemark->next_prediction()) {
       # $gene is an instance of Bio::Tools::Prediction::Gene, which inherits
       # off Bio::SeqFeature::Gene::Transcript.
       #
       # $gene->exons() returns an array of
       # Bio::Tools::Prediction::Exon objects
       # all exons:
       @exon_arr = $gene->exons();

       # initial exons only
       @init_exons = $gene->exons('Initial');
       # internal exons only
       @intrl_exons = $gene->exons('Internal');
       # terminal exons only
       @term_exons = $gene->exons('Terminal');
       # singleton exons:
       ($single_exon) = $gene->exons();
   }

   # essential if you gave a filename at initialization (otherwise the file
   # will stay open)
   $Genemark->close();

no fr, that close() is ESSENTIAL if you gave a filename at initialization — otherwise the file just stays open forever like a situationship you never ended 😭

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🦋 DESCRIPTION 🦋

the Genemark module is your parser bestie for Genemark gene structure prediction output. it takes one gene prediction and turns it into a Bio::SeqFeature::Gene::Transcript-derived object. slay.

ngl, this module was developed around genemark.hmm for eukaryots v2.2a and will probably not work with other versions. so like… don't come for me if you use a different version 💀

it also implements the Bio::SeqAnalysisParserI interface, so it can be used wherever such an object fits. see Bio::SeqAnalysisParserI. iykyk 💅

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💜 FEEDBACK 💜

🎀 Mailing Lists 🎀

user feedback is an integral part of the evolution of this and other Bioperl modules — like, genuinely, we need you 🫶. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated, fr fr.

 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. give them the ✨full✨ tea so they can actually help you.

🐛 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, Mark Fiers 👑

email hlapp@gmx.net m.w.e.j.fiers@plant.wag-ur.nl

iconic authors, we stan 💖

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (you know, the lil underscore that says "not for you bestie, this is internal business" 🙈).

🔥 new

• Title — new
• Usage — my $obj = Bio::Tools::Genemark->new();
• Function — Builds a new Bio::Tools::Genemark object
• Returns — an instance of Bio::Tools::Genemark
• Args — seqname

🔥 analysis_method

• Usage — $Genemark->analysis_method();
• Purpose — Inherited method. Overridden to ensure that the name matches /GeneMark.hmm/i.
• Returns — String
• Argument — n/a

🔥 next_feature

• Title — next_feature
• Usage —

while($gene = $Genemark->next_feature()) {
         # do something
  }

• Function — Returns the next gene structure prediction of the Genemark 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 = $Genemark->next_prediction()) {
         # do something
  }

• Function — Returns the next gene structure prediction of the Genemark result file. Call this method repeatedly until FALSE is returned.
• Example —
• Returns — A Bio::Tools::Prediction::Gene object.
• Args —

🔥 _parse_predictions

• Title — _parse_predictions()
• Usage — $obj->_parse_predictions()
• Function — Parses the prediction section. Automatically called by next_prediction() if not yet done.
• Example —
• Returns —

🔥 _prediction

• Title — _prediction()
• Usage — $gene = $obj->_prediction()
• Function — internal
• Example —
• Returns —

🔥 _add_prediction

• Title — _add_prediction()
• Usage — $obj->_add_prediction($gene)
• Function — internal
• Example —
• Returns —

🔥 _predictions_parsed

• Title — _predictions_parsed
• Usage — $obj->_predictions_parsed
• Function — internal
• Example —
• Returns — TRUE or FALSE

🔥 _has_cds

• Title — _has_cds()
• Usage — $obj->_has_cds()
• Function — Whether or not the result contains the predicted CDSs, too.
• Example —
• Returns — TRUE or FALSE

🔥 _read_fasta_seq

• Title — _read_fasta_seq()
• Usage — ($id,$seqstr) = $obj->_read_fasta_seq();
• Function — Simple but specialised FASTA format sequence reader. Uses $self->_readline() to retrieve input, and is able to strip off the traling description lines.
• Example —
• Returns — An array of two elements.

🔥 _seqname

• Title — _seqname
• Usage — $obj->_seqname($seqname)
• Function — internal
• Example —
• Returns — String

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and that's the whole page bestie, you ate that 💅✨ this little gem is from perl v5.32.1, dated 2021-08-15, and it lives under the name Bio::T...nemark(3pm) in the User Contributed Perl Documentation. go forth and parse some genes, main character 🌸🦋💖