Bio::A...::pfam(3pm)

✨ NAME ✨

Bio::AlignIO::pfam — it's the pfam sequence input/output stream, bestie 💖 and also, yes, the manual page you're reading right now is filed under Bio::A...::pfam (the terminal shortened it, it's giving mystery novel title fr fr 🙈).

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🌸 SYNOPSIS 🌸

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

Okay so real talk — do not come for this module directly. It does not want to be perceived like that. You go through the Bio::AlignIO class, periodt 💅.

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🦋 DESCRIPTION 🦋

This object can transform Bio::SimpleAlign objects to and from pfam flat file databases. That's the whole gig, and honestly? It ate. ✨

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💌 FEEDBACK 💌

🫶 Support 🫶

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. 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. No cap, the more detail you give, the faster somebody can help you out 🎀

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

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

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👑 AUTHORS - Peter Schattner 👑

Email: schattner@alum.mit.edu 💖

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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 "backstage pass only" marker, iykyk 🌈

⭐ next_aln ⭐

• Title : next_aln
• Usage : $aln = $stream->next_aln()
• Function: returns the next alignment in the stream
• Returns : L<Bio::Align::AlignI> object
• Args : NONE

Give it zero arguments and it hands you back the next alignment in the stream, as a L<Bio::Align::AlignI> object. Slay 💅

🌟 write_aln 🌟

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

Feed it a L<Bio::Align::AlignI> object and it writes that $aln into the stream. You get 1 if it worked and 0 if it flopped — so like, check your return value bestie, don't just assume 😭

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And that's the page!! This little gem shipped with perl v5.32.1, dated 2021-08-15, and the footer stamped it Bio::A...::pfam(3pm) — so yeah, that's the vibe check, we're done here, go write some alignments 🧚💜