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

💖 NAME 💖

Bio::AlignIO::xmfa — the XMFA MSA sequence input/output stream, bestie. Yes that's the whole name. Slay.

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✨ SYNOPSIS ✨

Okay so listen. Do not use this module directly. Like, at all. Use it via the Bio::AlignIO class, periodt.

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🦋 DESCRIPTION 🦋

This object can transform Bio::SimpleAlign objects from XMFA flat file databases. That's its whole thing and it eats every time.

Want the tea on the format? It's all right here:

http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html

Also, full transparency: this module is based on the AlignIO::fasta parser written by Peter Schattner. Credit where credit is due, we love an icon. 👑

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🎀 TODO 🎀

The to-do list, no cap:

• Finish write_aln()
• Clean up code
• Allow LargeLocatableSeq (e.g. for very large sequences from Mauve)

It's giving "work in progress" and honestly? Same.

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🫶 FEEDBACK 🫶

🌸 Support 🌸

If you have usage questions or support issues, please direct them to the mailing list:

bioperl-l@bioperl.org

and not straight to the module maintainer. The way that there are so many experienced and responsive experts on that list who will look at your problem and quickly address it — use them, they're the main characters here. 💅

Please include a thorough description of the problem with code and data examples if at all possible. Fr fr, the more detail the better.

🐛 Reporting Bugs 🐛

Report bugs to the Bioperl bug tracking system so we can keep track of 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 👑

Chris Fields

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💀 APPENDIX 💀

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ — iykyk, that underscore means "bestie this is internal, handle with care".

💜 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

🔥 write_aln

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

See Bio::Align::AlignI

🧚 _get_len

• Title — _get_len
• Usage — (blank, the original leaves this one empty, no notes given 🙈)
• Function — determine number of alphabetic chars
• Returns — integer
• Args — sequence string

⭐ 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, bestie! 💖 This lil masterpiece shipped with perl v5.32.1, dated 2021-08-15, from the Bio::A...::xmfa(3pm) manual page. Go forth and align your XMFA files, you absolute legend. 🌈🦋✨