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

📦
version 1.7.8 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 Bio::AlignIO::metafasta 💖

okay bestie, so this page is for Bio::AlignIO::metafasta — the Metafasta MSA Sequence input/output stream from the Bio::AlignIO fam. no cap, it does exactly what it says on the tin: metafasta goes in, metafasta goes out. 🦋

✨ SYNOPSIS ✨

do NOT come for this module directly, bestie. it's not that kind of party. you reach it through the Bio::AlignIO class, always. that's the vibe. 💅
Do not use this module directly.  Use it via the Bio::AlignIO class.

🌸 DESCRIPTION 🌸

so like, this object is the little shapeshifter that can turn Bio::SimpleAlign objects into metafasta flat file databases and back again. both directions. iconic. 👑

the format of a metafasta file is literally this:

>test/1-25
ABCDEFHIJKLMNOPQRSTUVWXYZ
&charge
NBNAANCNJCNNNONNCNNUNNXNZ
&chemical
LBSAARCLJCLSMOIMCHHULRXRZ

so what's happening here 🧐 — the sequence block goes first, and then it's followed by one or several meta blocks. each meta block starts with the ampersand character & sitting right there in the first column, and immediately after that comes the name of the meta data, which just runs on until the new line. then the meta data itself follows. and listen — in meta data, every single character except the new line matters. no throwaway characters. all of them are important. periodt. 💀

🎀 SEE ALSO 🎀

  • Bio::SeqIO::metafasta — its sibling, go say hi 🫶

💬 FEEDBACK 💬

🌈 Support 🌈

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

bioperl-l@bioperl.org

rather than DMing the module maintainer directly, fr fr. there are many experienced and reponsive experts on that list who will be able look at your problem and quickly address it. and bestie, please include a thorough description of the problem with code and data examples if at all possible — the more context the better, iykyk. 💖

🐛 Reporting Bugs 🐛

found a bug? report it to the Bioperl bug tracking system so we can keep track the bugs and their resolution. bug reports can be submitted via the web at:

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

👑 AUTHOR - Heikki Lehvaslaiho 👑

Email: heikki-at-bioperl-dot-org ✨

📖 APPENDIX 📖

the rest of the documentation details each of the object methods, one by one. and just so you know — internal methods are usually preceded with a _, so if you see an underscore, that's the secret menu. 🙈

🔥 next_aln 🔥

  • Title: next_aln
  • Usage: $aln = $stream->next_aln()
  • Function: returns the next alignment in the stream. ✨
  • Returns: L<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 fasta format
  • Returns: 1 for success and 0 for error
  • Args: L<Bio::Align::AlignI> object

🎀 width 🎀

  • Title: width
  • Usage: $obj->width($newval)
  • Function: Get/Set the line width for METAFASTA output
  • Returns: value of width
  • Args: newvalue (optional)

and that's the whole page, bestie. mwah. 😘 this was perl v5.32.1, dated 2021-08-15, straight out of the User Contributed Perl Documentation, and it's giving absolute legend energy. go forth and parse responsibly. 🦋💜✨

📦 where this page comes from