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

💖 Bio::T...Eponine — the manual, but make it a group chat 💖

okay bestie, so this is the perl doc page for Bio::T...Eponine, from the User Contributed Perl Documentation collection. yes the title is literally Bio::T...Eponine(3pm) — the dots are doing their own thing and we respect them 🫶

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✨ NAME ✨

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

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🌸 SYNOPSIS 🌸

here's the whole thing, verbatim, no cap:

use Bio::Tools::Eponine;
use strict;
   my $seq = "/data/seq.fa";
   my $threshold  = "0.999";
   my @params = ( -seq => $seq,
                  -threshold => $threshold);

  my $factory = Bio::Tools::Run::Eponine->new(@params);
    # run eponine against fasta
       my $r = $factory->run_eponine($seq);
       my $parser = Bio::Tools::Eponine->new($r);

      while (my $feat = $parser->next_prediction){
               #$feat contains array of SeqFeature
              foreach my $orf($feat) {
                  print $orf->seq_id. "\n";
              }
      }

like. look at her go. $feat is carrying an array of SeqFeature and we're just printing $orf->seq_id for each one. iconic behavior tbh ✨

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🦋 DESCRIPTION 🦋

so this is a parser for Eponine — and Eponine is a probabilistic transcription start site detector that's optimized for mammalian genomic sequence. 🧬

the way this module works: it inherits off Bio::Tools::AnalysisResult, which means it implements Bio::SeqAnalysisParserI. if you wanna go read up on those, they're right there — Bio::Tools::AnalysisResult and Bio::SeqAnalysisParserI. iykyk 💜

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🎀 FEEDBACK 🎀

💌 Mailing Lists

okay so user feedback is an integral part of how this module and all the other Bioperl modules evolve. so please, send your comments and suggestions to one of the Bioperl mailing lists. your participation is much appreciated — like genuinely, they mean it 🫶

 bioperl-l@bioperl.org                  - General discussion
 http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

🩹 Support

usage questions and support issues? send them to the mailing list:

bioperl-l@bioperl.org

not to the module maintainer directly, bestie. that's the rule. the reason is lowkey wholesome: there are lots of experienced and responsive experts on the list who'll be able to look at your problem and address it quickly. ⭐

and please, if it's at all possible, include a thorough description of the problem plus code and data examples. thorough. we're begging 🙈

🐛 Reporting Bugs

found a bug? report it to the Bioperl bug tracking system — that's how they keep track of the bugs and their resolutions. bug reports go in via the web:

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

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👑 AUTHOR - Tania Oh 👑

<gisoht-at-nus.edu.sg>

periodt. that's the author. 💖

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🌈 APPENDIX 🌈

the rest of this doc details each of the object methods, one by one. and heads up: internal methods are usually preceded with a _ — so if you see an underscore, that's your little signal that it's internal business 🤫

🍓 analysis_method

• Usage — $mzef->analysis_method();
• Purpose — an inherited method! but it's overridden so that the name matches /mzef/i.
• Returns — String
• Argument — n/a

🍓 next_feature

• Title — next_feature
• Usage — while($gene = $mzef->next_feature()) { # do something }
• Function — returns the next gene structure prediction of the MZEF result file. call this method repeatedly until FALSE comes back.

the object you get back is actually a SeqFeatureI implementing object. this method is required for classes implementing the SeqAnalysisParserI interface, and at present it's merely an alias for next_prediction().

also important: with the present version of MZEF, there will only be one object returned, because MZEF doesn't predict individual genes — it just predicts potential internal exons. one (1) object. that's it. 🫠

• Example — (empty)
• Returns — a Bio::Tools::Prediction::Gene object.
• Args — (empty)

🍓 next_prediction

• Title — next_prediction
• Usage — while($gene = $mzef->next_prediction()) { # do something }
• Function — returns the next gene structure prediction of the MZEF result file. call this method repeatedly until FALSE comes back.

note that with the present version of MZEF there will only be one object returned, because MZEF does not predict individual genes, it just does potential internal exons. same energy as above. 🧚

• Example — (empty)
• Returns — a Bio::Tools::Prediction::Gene object.
• Args — (empty)

🍓 _parse_predictions

• Title — _parse_predictions()
• Usage — $obj->_parse_predictions()
• Function — parses the prediction section. it's automatically called by next_prediction() if that hasn't happened yet.
• Example — (empty)
• Returns — (empty)

🍓 create_feature

• Title — create_feature
• Usage — obj->create_feature($feature)
• Function — returns an array of features
• Returns — returns an array of features
• Args — none

🍓 _prediction

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

🍓 _predictions_parsed

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

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and that's the whole page, bestie!! 🎀✨ thanks for reading, you're doing amazing, and this doc was generated by perl v5.32.1 back on 2021-08-15. she's vintage. she's iconic. she's Bio::T...Eponine(3pm) and we're obsessed. mwah 💅💖