Bio::S...:hmmer(3pm)

🌸 NAME 🌸

okay bestie, gather round, this is Bio::SearchIO::hmmer — a whole parser for HMMER2 and HMMER3 output 💅 and it handles the big three: hmmscan, hmmsearch, and hmpfam. (yes it says hmmpfam in the source, no I will not be correcting the vibes, it's iconic 💖)

Also, real talk, the page you're reading right now is Bio::S...:hmmer(3pm) from the User Contributed Perl Documentation collection, iykyk.

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✨ SYNOPSIS ✨

listen, do NOT use this class directly, bestie, it's not that kind of relationship 😭 it's available through Bio::SearchIO:

# do not use this class directly it is available through Bio::SearchIO
use Bio::SearchIO;
my $in = Bio::SearchIO->new(-format => 'hmmer',
                            -file   => 't/data/L77119.hmmer');
while( my $result = $in->next_result ) {
    # this is a Bio::Search::Result::HMMERResult object
    print $result->query_name(), " for HMM ", $result->hmm_name(), "\n";
    while( my $hit = $result->next_hit ) {
        print $hit->name(), "\n";
        while( my $hsp = $hit->next_hsp ) {
            print "length is ", $hsp->length(), "\n";
        }
    }
}

look at that nesting. main character energy, honestly 🫶

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🦋 DESCRIPTION 🦋

This object is a parser for HMMER output, periodt. It works with both HMMER2 and HMMER3 — yes both, she contains multitudes ✨

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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 the Bioperl mailing list. Your participation is much appreciated 💖

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. There are so many experienced and responsive experts who will be able to look at the problem and quickly address it — like, that's the whole point, bestie. And please include a thorough description of the problem with code and data examples if at all possible 🙏 (the more context the better, no cap)

🐛 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

lowkey the most helpful thing you'll ever do for a maintainer 💜

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👑 AUTHOR - Kai Blin 👑

Email: kai.blin-at-biotech.uni-tuebingen.de 🌈

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📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ 💀 (yes, the underscore is the secret handshake, that's just how it is)

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and that's the whole page, bestie!! this was Bio::S...:hmmer(3pm), generated with perl v5.30.0 on 2019-10-29 — dated but still slaying 💅✨ go parse something cute 🦋💖