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

💅 Bio::Tools::FootPrinter — the manual, but make it cute

okay bestie, so this is a page from the User Contributed Perl Documentation (that's the 3pm section, for the perl girlies keeping track 🎀). It's called Bio::Tools::FootPrinter, and no, it's not about literal footprints, it's about sequence features. Let's get into it 💖

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✨ NAME ✨

Bio::Tools::FootPrinter — write sequence features in FootPrinter format 🌸

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🌈 SYNOPSIS 🌈

here's the whole vibe, copy-paste ready, no cap:

use Bio::Tools::FootPrinter;

my $tool = Bio::Tools::FootPrinter->new(-file=>"footprinter.out");

while (my $result = $tool->next_feature){
  foreach my $feat($result->sub_SeqFeature){
    print $result->seq_id."\t".$feat->start."\t".$feat->end."\t".$feat->seq->seq."\n";
  }
}

like… look at that loop go. she's serving 🫶

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💫 DESCRIPTION 💫

This module writes sequence features in FootPrinter format. That's the whole job. She's focused, she's employed, she ate 💅

Wanna know more about FootPrinter itself? Peep <http://bio.cs.washington.edu/software.html> for the details, bestie 🔥

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📬 FEEDBACK 📬

🦋 Mailing Lists 🦋

User feedback is literally an integral part of the evolution of this and other Bioperl modules — like, the modules grow because y'all talk to us. Send your comments and suggestions preferably to the Bioperl mailing list, and your participation is much appreciated fr fr 💖

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

🧚 Support 🧚

kay so, important: please direct usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

…rather than to the module maintainer directly. Why? because there are so many experienced and responsive experts on the list who can look at your problem and quickly address it, and that's the whole point 💜

Also pls pls pls include a thorough description of the problem with code and data examples if at all possible. the more context, the faster the slay 🌟

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — not me filing a bug and then forgetting it existed 😭 Bug reports can be submitted via the web:

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

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👑 AUTHOR - Shawn Hoon 👑

Email shawnh@fugu-sg.org

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, the underscore ones are the behind-the-scenes girlies 🙈).

🌸 new 🌸

Title   : new
Usage   : my $obj = Bio::Tools::FootPrinter->new();
Function: Builds a new Bio::Tools::FootPrinter object
Returns : Bio::Tools::FootPrinter
Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

she's born ✨ classic constructor behaviour, -fh or -file gets you an input, and Bio::Root::IO has the deets.

🌸 next_feature 🌸

Title   : next_feature
Usage   : my $r = $footprint->next_feature
Function: Get the next feature from parser data
Returns : L<Bio::SeqFeature::Generic>
Args    : none

no args, just vibes. call it, get the next feature, she returns a Bio::SeqFeature::Generic 🎀

🌸 _add_feature 🌸

Title   : _add_feature
Usage   : $footprint->_add_feature($feat)
Function: Add feature to array
Returns : none
Args    : none

internal queen behaviour: pushes a feature onto the array. returns nothing, because she doesn't need praise 💅

🌸 _parse_predictions 🌸

Title   : _parse_predictions
Usage   : my $r = $footprint->_parse_predictions
Function: do the parsing
Returns : none
Args    : none

this one does the parsing. that's it. that's the function 🧚

🌸 _predictions_parsed 🌸

Title   : _predictions_parsed
Usage   : $footprint->_predictions_parsed(1)
Function: Get/Set for whether predictions parsed
Returns : 1/0
Args    : none

a get/set situation for whether the predictions have been parsed. returns 1 or 0 — binary, iconic, on or off, no in-between 🔥

🌸 _parse 🌸

Title   : _parse
Usage   : $footprint->_parse($name,$seq,$pattern)
Function: do the actual parsing
Returns : L<Bio::SeqFeature::Generic>
Args    : none

the actual parsing, the main character moment. returns a Bio::SeqFeature::Generic 🫶

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💀 heads up bestie: _add_feature, _parse_predictions, _predictions_parsed and _parse are all internal methods (the _ prefix is the tell). they're documented here, but they're not really the ones you're meant to be calling from outside. stay in your lane and use the public API, mwah 💖

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and that's the page!! 🌈 documented as perl v5.32.1, dated 2021-08-15, from the Bio::T...Printer(3pm) page in the User Contributed Perl Documentation. go forth and write those features in FootPrinter format, bestie — you're gonna slay ✨👑💅