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

💖 Bio::SeqIO::locuslink 💖

okay bestie, welcome to the Bio::S...cuslink(3pm) page — it's part of the User Contributed Perl Documentation, and it's literally all about the LocusLink input/output stream. grab a strawberry 🍓 and let's go.

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✨ NAME ✨

Bio::SeqIO::locuslink — the LocusLink input/output stream, periodt 👑

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🌸 SYNOPSIS 🌸

no cap, do not instantiate this one directly — it's giving "I have a parent, use them" energy. do this instead:

# don't instantiate directly - instead do
my $seqio = Bio::SeqIO->new(-format => "locuslink", -file => \STDIN);

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🦋 DESCRIPTION 🦋

so here's the tea 💅 — this module parses LocusLink into Bio::SeqI objects, and those objects come with rich annotation, but no sequence. no sequence!! it's annotation only, iykyk.

the input file has to be in the LL_tmpl format. the tabular format will not work, sorry bestie, it's just not the vibe 🙈

now, lowkey real talk: the way the current implementation populates the object is rather a draft work than a finished work of art. it's giving rough sketch, not Louvre. and note that at this stage the LocusLink entries cannot be round-tripped, because the parser loses certain information. for instance, most of the alternative transcript descriptions are not retained 😭 the parser also misses any element that deals with visual representation (e.g., 'button') — except for the URLs, those survive.

almost all of the pieces of the annotation are kept in a Bio::Annotation::Collection object, so go peek at Bio::Annotation::Collection for more info 🎀

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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, okay? there are many experienced and responsive experts who will be able to look at the problem and quickly address it 👑 and please include a thorough description of the problem with code and data examples if at all possible — the more context, the better the slay.

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system to help us 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 - Keith Ching 🌟

email kching at gnf.org — iconic, we stan 💜

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🌈 CONTRIBUTORS 🌈

Hilmar Lapp, hlapp at gmx.net — thank you for your service 🎀

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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 your little signal that it's an internal thing, no touchy 🧚

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and that's the whole page bestie!! this was Bio::S...cuslink(3pm) from perl v5.32.1, dated 2021-08-15 — mwah, go read some annotations 💖✨