Bio::A...IO::msf(3pm)

💖 NAME 💖

Bio::AlignIO::msf — the msf sequence input/output stream, bestie. that's it, that's the whole vibe 🦋

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✨ SYNOPSIS ✨

okay so listen. do NOT use this module directly, fr fr. like, not even once. you go through the Bio::AlignIO class instead, okay? that's the whole move 💅

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🌸 DESCRIPTION 🌸

this object is literally a glow-up machine: it transforms Bio::Align::AlignI objects to and from msf flat file databases. in and out. back and forth. iconic behavior honestly 🎀

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🫶 FEEDBACK 🫶

💌 Support 💌

got a usage question? a support issue? a little "why is this not working" moment? 😭 send it to the mailing list:

bioperl-l@bioperl.org

and NOT to the module maintainer directly, bestie, i'm begging. there are so many experienced and responsive experts on that list who will look at your problem and be like "oh yeah, here's the fix" so fast ✨

and pls pls pls include a thorough description of the problem along with your code and data examples if at all possible. like, all of it. the more context the better, no cap 🫶

🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so we can keep track of the bugs and their resolutions. we're keeping receipts, but the cute kind 💅

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 is about to detail each of the object methods, one by one. and heads up: internal methods are usually preceded with a _, so if you see an underscore just know it's giving "backstage, not main character energy" 🙈

🧚 next_aln 🧚

• Title : next_aln
• Usage : $aln = $stream->next_aln()
• Function: returns the next alignment in the stream. Tries to read all MSF. It reads all non whitespace characters in the alignment area. For MSFs with weird gaps (eg ~~~) map them by using $aln->map_chars('~','-')
• Returns : Bio::Align::AlignI object
• Args : NONE

💜 write_aln 💜

• Title : write_aln
• Usage : $stream->write_aln(@aln)
• Function: writes the $aln object into the stream in MSF format. Sequence type of the alignment is determined by the first sequence.
• Returns : 1 for success and 0 for error
• Args : Bio::Align::AlignI object

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perl v5.32.1 · 2021-08-15

and that's the whole page, bestie 💖 this was User Contributed Perl Documentation, brought to you by Bio::A...IO::msf(3pm), dated 2021-08-15, running on perl v5.32.1. slay, go read your alignments 🎀✨🦋