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

🌸 Bio::T...Hmmpfam(3pm) 💅

User Contributed Perl Documentation · Bio::T...Hmmpfam(3pm)

okay bestie, sit down, hydrate, and let me tell you about the most specific little parser you're ever gonna meet 🫶

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✨ NAME ✨

Bio::Tools::Hmmpfam — it's a Parser for Hmmpfam program. that's the whole job. she parses. she does it well. periodt. 💅

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🎀 SYNOPSIS 🎀

here's the vibe, copy-paste ready, no thoughts head empty:

use Bio::Tools::Hmmpfam;
my @hmmpfam_feat;
my $hmmpfam_parser = Bio::Tools::Hmmpfam->new(-fh =>$filehandle );
while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) {
      push @hmmpfam_feat, $hmmpfam_feat;
}

make a parser, hand it a filehandle, loop over next_result until it stops giving, shove everything into @hmmpfam_feat. that's it. that's the whole ritual. 🦋

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🌈 DESCRIPTION 🌈

Parser for Hmmpfam program. lowkey that's the entire pitch. also, see also Bio::SearchIO::hmmer — go look at her too, she's the other icon in this friend group. ✨

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💌 FEEDBACK 💌

📬 Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. not to be dramatic but your comments and suggestions are literally the main character of this whole project's glow-up. send them 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

okay so if you have a usage question or a support issue, please direct it to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. and this is not a shady thing, it's a strategy bestie — many experienced and reponsive experts will be able look at the problem and quickly address it. (yes, "reponsive", that's the original spelling, we do not touch the sacred text 💀)

please include a thorough description of the problem with code and data examples if at all possible. no vague "it broke 😭" DMs. give us the receipts. 🧾

🐛 Reporting Bugs

found a bug? report it 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

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👑 AUTHOR - Balamurugan Kumarasamy 👑

Email: fugui@worf.fugu-sg.org

the literal legend who wrote this. we stan. 🌟

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📖 APPENDIX 📖

the rest of the documentation details each of the object methods. and heads up — internal methods are usually preceded with a _, so if you see an underscore, that's the "do not perceive me" energy. 🙈

🧚 new

• Title — new
• Usage — my $obj = Bio::Tools::Hmmpfam->new(-fh=>$filehandle);
• Function — Builds a new Bio::Tools::Hmmpfam object
• Returns — Bio::Tools::Hmmpfam
• Args — -filename, -fh (filehandle)

birth of an object. iconic behavior. ✨

🍓 next_result

• Title — next_result
• Usage — my $feat = $hmmpfam_parser->next_result
• Function — Get the next result set from parser data
• Returns — L<Bio::SeqFeature::Generic>
• Args — none

call her in a loop and she keeps handing you results until she's out. no args, no drama. 💅

🦋 create_feature

• Title — create_feature
• Usage — my $feat=$hmmpfam_parser->create_feature($feature,$seqname)
• Function — creates a SeqFeature Generic object
• Returns — L<Bio::SeqFeature::Generic>
• Args — (empty, she takes nothing on paper, but the usage line says otherwise, iykyk) 🙈

🎀 seqname

• Title — seqname
• Usage — obj->seqname($seqname)
• Function — Internal(not to be used directly)
• Returns — (nothing listed)
• Args — seqname

Internal(not to be used directly) — bestie this one said "don't perceive me" in the docs AND meant it. respect the boundary. 🫶

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and that's the whole page, no cap, every single line of it 💖

this doc is brought to you by perl v5.30.0, dated 2019-10-29, and filed under Bio::T...Hmmpfam(3pm). ok bye bestie, go parse something gorgeous 🌸✨👑