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

💖 NAME 💖

Bio::Tools::RepeatMasker — it's a parser for RepeatMasker output, bestie. That's the whole vibe. It lives in the 3pm section of the manual, aka the Perl module pages, so you know it's giving library energy. 🧚

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✨ SYNOPSIS ✨

Okay so here's the whole thing, copy it, run it, slay:

use Bio::Tools::RepeatMasker;
my $parser = Bio::Tools::RepeatMasker->new(-file => 'seq.fa.out');
while( my $result = $parser->next_result ) {
  # get some value
}

You spin up the parser, you loop over next_result, you grab whatever values you need. Simple. Iconic. No cap.

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🌸 DESCRIPTION 🌸

A parser for RepeatMasker output. That's it, that's the description, she's lowkey minimal but she does her job 💅

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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 whole ecosystem grows because people speak up. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. Fr fr. 🥺

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. Like, pls bestie, the maintainer is one person. Many experienced and reponsive 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, that's the vibe check. ✨

🐛 Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution — so they actually get fixed and not just lost in the void 💀 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

Shoutout to Shawn, the main character who built this 💜

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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 the "do not touch, this is backstage" marker, iykyk.

⭐ new

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

It builds you a brand new Bio::Tools::RepeatMasker object, returns that same class back, and you feed it -fh or -file with a $val to init the input — peek at Bio::Root::IO for the whole story on that. 🎀

🦋 next_result

Title   : next_result
Usage   : my $r = $rpt_masker->next_result
Function: Get the next result set from parser data
Returns : Bio::SeqFeature::FeaturePair
          Feature1 is the Query coordinates and Feature2 is the Hit
Args    : none

Grab the next result set from the parser data. You get back a Bio::SeqFeature::FeaturePair — and heads up, Feature1 is the Query coordinates while Feature2 is the Hit. No args, she takes nothing. 🫶

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💖 okay that's the whole page, you're officially a RepeatMasker parser girlie now 💖

This was brought to you by perl v5.32.1, dated 2021-08-15, straight from the User Contributed Perl Documentation. Stay slay, bestie 💅✨🎀