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

🧬 Bio::Tools::Genomewise — the vibe check

okay bestie, so this page is from the User Contributed Perl Documentation corner of the world, and it's all about Bio::Tools::Genomewise(3pm) — literally the results of one Genomewise run. pull up a chair, we're parsing 💅

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✨ NAME ✨

Bio::Tools::Genomewise — the results of one Genomewise run. that's it, that's the whole name. short. iconic. no notes. 👑

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🌸 SYNOPSIS 🌸

here's how you actually use it, bestie — copy-paste, don't improvise:

use Bio::Tools::Genomewise;
my $gw = Bio::Tools::Genomewise(-file=>"genomewise.out");

while (my $gene = $gw->next_prediction){
    my @transcripts = $gene->transcripts;
    foreach my $t(@transcripts){
      my @exons =  $t->exons;
      foreach my $e(@exons){
          print $e->start." ".$e->end."\n";
      }
    }
}

look at that nested loop go. she's serving structure. 🦋

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💖 DESCRIPTION 💖

so this is the parser for the output of Genewise. she takes either a file handle or a file name, and hands you back a Bio::SeqFeature::Gene::GeneStructure object. cute, right?

but listen — you will need to specify the proper target sequence id on the object yourself, like this:

$feature->seq_id($seqid);

don't skip that step, it's giving "forgot the password" energy otherwise. 🔐

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is 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, genuinely 🥹

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 responsive 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 — the more deets the better, bestie, we love a detailed bug report.

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution. bug reports can be submitted via the web:

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

not me filing a bug report with zero context… bestie please, include the examples 🙈

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👑 AUTHOR - Fugu Team, Jason Stajich

Email:

fugui-at-worf.fugu-sg.org
jason-at-bioperl-dot-org

two legends, one module. slay. 💜

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🎀 APPENDIX 🎀

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _ — that underscore is basically a "staff only" door, iykyk.

⭐ new

• Title: new
• Usage:

$obj->new(-file=>"genewise.out");
$obj->new(-fh=>\*GW);

• Function: constructor for genomewise wrapper. takes either a file or filehandle.
• Example: (none given, bestie, the original left it blank)
• Returns: Bio::Tools::Genomewise

⭐ _get_strand

• Title: _get_strand
• Usage: $obj->_get_strand
• Function: takes start and end values, swaps them if start>end and returns end
• Example: (blank in the original)
• Returns: $start,$end,$strand

⭐ score

• Title: score
• Usage: $obj->score
• Function: get/set for score info
• Example: (blank in the original)
• Returns: a score value

⭐ _prot_id

• Title: _prot_id
• Usage: $obj->_prot_id
• Function: get/set for protein id
• Example: (blank in the original)
• Returns: a protein id

⭐ _target_id

• Title: _target_id
• Usage: $obj->_target_id
• Function: get/set for genomic sequence id
• Example: (blank in the original)
• Returns: a target id

⭐ next_prediction

• Title: next_prediction
• Usage:

while($gene = $genewise->next_prediction()) {
        # do something
}

• Function: returns the gene structure prediction of the Genomewise result file. call this method repeatedly until FALSE is returned.
• Example: (blank in the original)
• Returns: a Bio::SeqFeature::Gene::GeneStructure object
• Args: (blank in the original)

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and that's the whole page, bestie!! this one was documented by perl v5.32.1 and dated 2021-08-15 — so yeah, she's been around, and she still hits. go parse some genomes, you've got this 🧚💖✨