Bio::SeqIO::ace(3pm)

💖 Bio::SeqIO::ace 💖

okay bestie, gather round, because we're talking about Bio::SeqIO::ace(3pm) — the ace sequence input/output stream from the one and only User Contributed Perl Documentation. it's giving bioperl, it's giving file-format chaos, and honestly? it's iconic.

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✨ NAME ✨

Bio::SeqIO::ace — the ace sequence input/output stream, periodt. 💅

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🌸 SYNOPSIS 🌸

real talk, do not use this module directly. like, at all. use it via the Bio::SeqIO class instead, iykyk. 🫶

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🦋 DESCRIPTION 🦋

so this object can transform Bio::Seq objects to and from ace file format. that's the whole vibe. ✨

it only parses a DNA or Peptide objects contained in the ace file, producing PrimarySeq objects from them. everything else chillin' in the file? ignored. not our problem, not our era. 💀

and it doesn't attempt to parse any annotation attached to the containing Sequence or Protein objects — which would probably be impossible anyway, since everyone's ACeDB schema can be different. no two schemas are wearing the same outfit, and we respect that. 🙈

it also won't parse ace files containing Timestamps correctly either. lowkey tragic, but it can easily be added if considered necessary. just saying. 👑

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💌 FEEDBACK 💌

Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules — no cap. send your comments and suggestions preferably to one of the Bioperl mailing lists. your participation is much appreciated. 🥹

bioperl-l@bioperl.org                  - General discussion
http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

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

bioperl-l@bioperl.org

rather than to the module maintainer directly. bestie, there are so many experienced and responsive experts there who will be able look at the problem and quickly address it. please include a thorough description of the problem with code and data examples if at all possible. the more detail, the more slay. 🔥

Reporting Bugs

report bugs to the Bioperl bug tracking system to help us 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 - James Gilbert 👑

Email: jgrg@sanger.ac.uk

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🌈 APPENDIX 🌈

the rest of the documentation details each of the object methods. internal methods are usually preceded with a _. 👀

next_seq

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

next one up, bestie. no arguments, no drama. 💜

write_seq

Title   : write_seq
Usage   : $stream->write_seq(@seq)
Function: writes the $seq object into the stream
Returns : 1 for success and 0 for error
Args    : Bio::Seq object(s)

it writes the $seq object into the stream. returns 1 for success and 0 for error — binary queen behavior. 💅

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reminder: don't call this module directly, use Bio::SeqIO, and maybe don't feed it Timestamps unless someone actually adds that. 😭

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and that's the whole page, bestie!! this was Bio::SeqIO::ace(3pm) from perl v5.32.1, dated 2021-08-15 — so when you cite it, cite it cute. 🎀 bye pookie, go parse something iconic! ✨🦋💖