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

💖 NAME 💖

Bio::AlignIO::largemultifasta — the largemultifasta MSA sequence input/output stream, and yes bestie it is exactly as niche as it sounds 💅

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✨ SYNOPSIS ✨

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

fr fr. do NOT come for this module directly, she does not want to be touched. go through the Bio::AlignIO class like a normal person 🫶

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🦋 DESCRIPTION 🦋

okay so here's the vibe: this object can transform Bio::SimpleAlign objects to and from largemultifasta flat file databases. that's her whole job and she eats every time.

but listen — this is for the fasta sequence format, NOT the FastA analysis program. two completely different girlies, do not confuse them 😭 if you actually wanna process the pairwise alignments coming out of a FastA (FastX, FastN, FastP, tFastA, etc), you need to go hang out with the Bio::SearchIO module instead.

and the tea on this one: it's a reimplementation of the Bio::AlignIO::fasta modules, except she creates temporary files instead of keeping the whole entire sequences in memory. lowkey genius, highkey saving your RAM. main character resource management honestly 👑

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🎀 FEEDBACK 🎀

🌸 Support

please direct your usage questions and support issues to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer, okay? there are so many experienced and responsive experts on there who will look at your problem and address it fast, and the maintainer does not need to be in your DMs. if it's at all possible, please include a thorough description of the problem with code and data examples — the more detail the better, we love a thorough queen ✨

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution (tracking both is the whole point bestie). bug reports can be submitted via the web:

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

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👑 AUTHORS - Albert Vilella, Heikki Lehvaslaiho 👑

Email: avilella-at-gmail-dot-com, heikki-at-bioperl-dot-org

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📖 APPENDIX 📖

the rest of this documentation details each of the object methods. internal methods are usually preceded with a _ (iykyk, underscore = private business 💜)

💫 next_seq

• Title: next_seq
• Usage: $seq = $stream->next_seq()
• Function: returns the next sequence in the stream while taking care of the length
• Returns: Bio::Seq object
• Args: NONE

💫 next_aln

• Title: next_aln
• Usage: $aln = $stream->next_aln()
• Function: returns the next alignment in the stream.
• Returns: Bio::Align::AlignI object — returns 0 on end of file or on error
• Args: NONE

💫 write_aln

• Title: write_aln
• Usage: $stream->write_aln(@aln)
• Function: writes the $aln object into the stream in largemultifasta format
• 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 Bio::A...tifasta(3pm) energy right there 💖 thanks for reading the whole thing bestie, you ate that, periodt 🦋✨