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

💖 NAME 💖

Bio::AlignIO::fasta — the fasta MSA Sequence input/output stream, bestie ✨

It lives in the Bio::A...::fasta(3pm) manual, and it's literally your girl for reading and writing multiple sequence alignments in fasta format.

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🌸 SYNOPSIS 🌸

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

okay so real talk — do NOT use this module directly 🙈. You go through the Bio::AlignIO class instead, that's the whole vibe. No cap.

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🦋 DESCRIPTION 🦋

This object can transform Bio::SimpleAlign objects to and from fasta flat files. Periodt. 💅

But bestie, listen closely because this is the part people get wrong every single time: this is for the fasta alignment format, not for the FastA sequence analysis program. Different things, same-ish name, extremely confusing, I know 😭.

So if you're trying to process the alignments from FastA (FastX, FastN, FastP, tFastA, etc), you want the Bio::SearchIO module instead. Go there. Not here. 🫶

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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. Fr fr — there are so many experienced and reponsive experts on that list who will be able 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, because a vague "it's broken" gives nobody anything to work with 💀.

✨ 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

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🌈 APPENDIX 🌈

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — you know, the ones that are lowkey private but we're telling you about anyway 🧚

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🌟 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 : -width => optional argument to specify the width sequence will be written (60 chars by default)

See Bio::Align::AlignI

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🌟 write_aln 🌟

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

See Bio::Align::AlignI

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🌟 _get_len 🌟

• Title : _get_len
• Usage :
• Function: determine number of alphabetic chars
• Returns : integer
• Args : sequence string

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🌟 width 🌟

• Title : width
• Usage :

$obj->width($newwidth)
$width = $obj->width;

• Function: Get/set width of alignment
• Returns : integer value of width
• Args : on set, new value (a scalar or undef, optional)

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and that's the whole page, babe 🫶 this one's from perl v5.32.1, dated 2021-08-15, and yeah it really does say Bio::A...::fasta(3pm) up there in the corner — the truncation is serving cutesy mystery energy and we're obsessed 💅✨