Bio::AlignIO::po(3pm)

💖 Bio::AlignIO::po 💖

okay bestie, welcome to Bio::AlignIO::po — it's a po MSA Sequence input/output stream, and yes this page came to you courtesy of the User Contributed Perl Documentation crew (perl v5.32.1, dated 2021-08-15, but more on that at the end 🫶).

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✨ NAME ✨

Bio::AlignIO::po — a po MSA Sequence input/output stream. that's the whole name, she's simple, she's elegant, she slays 💅

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🌸 SYNOPSIS 🌸

⚠️ bestie LISTEN. Do not use this module directly. Use it via the Bio::AlignIO class. like, it's not a "you can't sit with us" thing, it's just how the plumbing works, iykyk 😭

Do not use this module directly.  Use it via the Bio::AlignIO class.

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🦋 DESCRIPTION 🦋

so what does this lil icon actually do? she can transform Bio::SimpleAlign objects to and from 'po' format flat file databases. periodt. 💖

and what even IS 'po' format? it's the native format of the POA alignment program — and here's the citation so you can be a good academic citizen about it, no cap:

Lee C, Grasso C, Sharlow MF, 'Multiple sequence alignment using partial order graphs', Bioinformatics (2002), 18(3):452-64

that's it, that's the vibe. she converts, she aligns, she leaves ✨

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💌 FEEDBACK 💌

🫶 Support 🫶

got questions? got support issues? please send them to the mailing list:

bioperl-l@bioperl.org

and NOT to the module maintainer directly, okay? no DMs to the maintainer, we keep it in the group chat 📵 there are so many experienced and reponsive experts on that list (yes, "reponsive", we keep the original spelling, we respect the original 💀) who will look at your problem and quickly address it. iconic behavior honestly.

also: if you possibly can, please include a thorough description of the problem with code and data examples. give them the full lore, bestie, not just "it's broken 😭". the more detail you bring, the faster someone fixes your thing. that's the deal 🎀

🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — both parts matter, tracking a bug without tracking its resolution is giving unfinished business fr fr.

bug reports can be submitted via the web:

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

go off, file it, you're doing amazing sweetie 💜

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👑 AUTHORS - Matthew Betts 👑

Email: matthew.betts@ii.uib.no

one author, one email, one legend. 🌟

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📖 APPENDIX 📖

the rest of this documentation goes into detail on each of the object methods. heads up: internal methods are usually preceded with a _ — so if you see an underscore, that's your cue that she's private and you should probably mind your business 🙈

💅 next_aln 💅

• Title — next_aln
• Usage — $aln = $stream->next_aln()
• Function — returns the next alignment in the stream.
• Returns — L<Bio::Align::AlignI> object — returns undef on end of file or on error
• Args — NONE

so you call her, she hands you the next alignment in the stream. if you hit the end of the file? undef. if something goes wrong? undef. either way you get undef, so like… vibe check your loop condition, bestie 😭 no arguments, she takes NONE, she needs nothing from you, she's low maintenance.

🎀 write_aln 🎀

• Title — write_aln
• Usage — $stream->write_aln(@aln)
• Function — writes the $aln object into the stream in po format
• Returns — 1 for success and 0 for error
• Args — L<Bio::Align::AlignI> object

this one takes your alignment object and writes it into the stream in po format. and the return? 1 if it ate, 0 if it did not. that's it, that's the whole API, no notes. 👑

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perl v5.32.1 · 2021-08-15 · that's the version and the date this page was born, and that's a wrap bestie 💖✨ you read the whole thing, you're literally the main character of documentation reading, go hydrate and go align something beautiful 🦋🌸