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

✨ Bio::T...::Match — the Bio::Tools::Match page, but make it make sense ✨

okay bestie, gather round, because we're reading a perl module doc and honestly? it's giving useful. this is Bio::Tools::Match from the User Contributed Perl Documentation collection, and it's about to become your new fave.

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💖 NAME 💖

Bio::Tools::Match — it parses the output that Transfac's match(TM) program spits out. that's the whole vibe. 🧬✨

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🌸 SYNOPSIS 🌸

here's the glow-up in code form, copy it exactly bestie:

use strict;

use Bio::Tools::Match;

my $parser = Bio::Tools::Match->new(-file => "match.out");

while (my $feat = $parser->next_result) {
  my $start = $feat->start;
  my $end = $feat->end;
  my $core_score = $feat->score;
  my $matrix_score = ($feat->annotation->get_Annotations('matrix_score'))[0]->value;
  my $matrix_id = ($feat->annotation->get_Annotations('matrix_id'))[0]->value;
}

like, look at her go. 💅

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🦋 DESCRIPTION 🦋

so this module exists to parse output from Transfac's match(TM) program. periodt.

⚠️ but listen — it does not support the histogram output of match. no cap, that's just not a thing it does. don't come for her about it. 💀

each result is a Bio::SeqFeature::Annotated representing a single matrix match. one match, one feature, one moment of main character energy. 👑

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🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — literally, they need your thoughts. send your comments and suggestions preferably to the Bioperl mailing list. your participation is so much appreciated, fr fr. 🥹

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

🌈 Support

okay so please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

...rather than to the module maintainer directly. the reason? many experienced and responsive experts will be able to look at the problem and quickly address it — like a group chat but everyone's a genius. 🧠✨

and please include a thorough description of the problem with code and data examples if at all possible. give them the full lore, bestie. 📖

🐛 Reporting Bugs

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

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

do it. it's iconic. 🐞💖

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👑 AUTHOR - Sendu Bala 👑

Email: bix@sendu.me.uk

(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 _. iykyk.

🎀 new

Title   : new
Usage   : my $obj = Bio::Tools::Match->new();
Function: Builds a new Bio::Tools::Match object
Returns : Bio::Tools::Match
Args    : -file (or -fh) should contain the contents of a standard match output

so new builds you a brand new Bio::Tools::Match object, and it hands one right back to you. 💫 the args? -file (or -fh) should contain the contents of a standard match output. that's the tea. ☕

🍓 next_result

Title   : next_result
Usage   : $result = $obj->next_result();
Function: Returns the next result available from the input, or undef if there
          are no more results.
Returns : Bio::SeqFeature::Annotated object. Features are annotated with tags
          for 'matrix_score', 'matrix_id' and a 'predicted' tag.
Args    : none

next_result gives you the next result available from the input — or undef if there are no more results, aka the vibe check failed and the list is empty. 😭

what you get back is a Bio::SeqFeature::Annotated object, and these features are annotated with tags for 'matrix_score', 'matrix_id' and a 'predicted' tag. no args needed. she just works. ✨

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and that's the whole page, bestie!! 🎀 this was Bio::T...::Match(3pm), documented under perl v5.32.1, dated 2021-08-15. go forth and parse those matches. slay. 💖🦋🌸👑