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

✨ Bio::T...Fgenesh(3pm) ✨

okay bestie, buckle up 💖 this is Bio::Tools::Fgenesh, straight out of the User Contributed Perl Documentation collection. it's a Perl module and it has ONE job and it does it gorgeously.

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🌸 NAME 🌸

Bio::Tools::Fgenesh — parse results of one Fgenesh run. that's it. that's the whole vibe. one run, one parse, no cap. 🎀

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🦋 SYNOPSIS 🦋

here's how you actually use it, copy-paste coded exactly like the original:

use Bio::Tools::Fgenesh;

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

# parse the results
# note: this class is-a Bio::Tools::AnalysisResult which implements
# Bio::SeqAnalysisParserI, i.e., $fgensh->next_feature() is the same
while($gene = $fgenesh->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)
$fgenesh->close();

lowkey important: if you handed it a filename at initialization, calling $fgenesh->close() is essential — otherwise the file just stays open forever. it's giving "left you on read" energy and we do not do that. 🙈

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💜 DESCRIPTION 💜

the Fgenesh module is a parser for Fgenesh (version 2) gene structure prediction output. it takes one gene prediction and turns it into a Bio::SeqFeature::Gene::Transcript-derived object. slay. 💅

and because it also implements the Bio::SeqAnalysisParserI interface, you can drop it in wherever an object like that fits. it's a social butterfly fr fr. 🦋

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🫶 FEEDBACK 🫶

💌 Mailing Lists 💌

user feedback is, like, 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 — genuinely, we're obsessed with you for it. 🥹

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. there are so many experienced and reponsive experts who will be able to 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. the more deets, the faster the fix. 💖

🐛 Reporting Bugs 🐛

report bugs to the Bioperl bug tracking system to help us keep track of 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 - Chris Dwan 👑

Email chris-at-dwan.org — say hi, he made this. 🌟

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk — underscore means "don't touch, that's my business"). 🙈

⭐ analysis_method ⭐

• Usage — $genscan->analysis_method();
• Purpose — inherited method. overridden to ensure that the name matches /genscan/i. (yes, genscan. that's what it says. iconic of it.)
• Returns — string
• Argument — n/a

⭐ next_feature ⭐

• Title — next_feature
• Usage —

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

• Function — returns the next gene structure prediction of the Fgenesh 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 = $fgenesh->next_prediction()) { ... }
• Function — returns the next gene structure prediction of the Genscan 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. it's proactive like that, main character energy. 👑
• 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: fasta_id & sequence

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and that's the whole page, bestie 💖 this one's perl v5.32.1, dated 2021-08-15, filed under Bio::T...Fgenesh(3pm). go parse something gorgeous. periodt. 💅✨🌸