Bio::S...rgeSeq(3pm)

💖 Bio::Seq::LargeSeq — the manual, but make it make sense 💖

okay bestie, so this is Bio::Seq::LargeSeq, a SeqI compliant object that stores sequence as files in /tmp. yeah. files. in /tmp. we're doing that. 💅

It lives in the Perl documentation, it's a user contributed thing, and the page is literally called Bio::S...rgeSeq(3pm) because apparently even the title got truncated (ironic, given what trunc does here, but whatever, we move).

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✨ NAME ✨

Bio::Seq::LargeSeq — a SeqI compliant object that stores sequence as files in /tmp.

no cap, that's the whole name section. iconic.

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✨ SYNOPSIS ✨

  # normal primary seq usage

that's it. that's the synopsis. the original really said "you know what, you'll figure it out" and honestly? respect. 🫶

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✨ DESCRIPTION ✨

So here's the vibe: this object stores a sequence as a series of files in a temporary directory. The whole point — the main character energy of this module — is letting someone store very large sequences (like, eg, > 100MBases) on a file system without running out of memory. And yes, the original literally specifies the scenario: eg, on a 64 MB real memory machine! 😭 a 64 MB machine. our ancestors suffered fr fr.

But listen, bestie, here's the catch — and it's a big one, so pay attention:

To actually make use of this functionality, the programs that use this object must not call $primary_seq->seq. If you do, the entire sequence will come out into memory and probably paste your machine. 💀

However (and this is the slay part), calls like $primary_seq->subseq(10,100) will cause only 90 characters to be brought into real memory. so it's giving lazy loading before lazy loading was cool. 👑

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✨ FEEDBACK ✨

🦋 Mailing Lists 🦋

User feedback is an integral part of the evolution of this and other Bioperl modules. 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. Many experienced and reponsive experts 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.

(yes, "reponsive" — that's the original's typo and I am not fixing it, we preserve the lore ✨)

🎀 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

please do this instead of just yelling into the void, bestie. the void does not have a ticket queue. 🐛

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✨ AUTHOR - Ewan Birney ✨

Email birney@ebi.ac.uk

shoutout Ewan, absolute legend, built this whole thing. 👑

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✨ APPENDIX ✨

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _. iykyk. 🔍

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✨ trunc ✨

• Title — trunc
• Usage — $subseq = $myseq->trunc(10,100);
• Function — Provides a truncation of a sequence,
• Example — (nothing, the original left this blank, and so shall we 🙈)
• Returns — a fresh Bio::SeqI object
• Args — (also blank. mysterious. we love a mystery. 💅)

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✨ Bio::Seq::LargePrimarySeq methods ✨

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✨ add_sequence_as_string ✨

• Title — add_sequence_as_string
• Usage — $seq->add_sequence_as_string("CATGAT");
• Function — Appends additional residues to an existing LargePrimarySeq object. This allows one to build up a large sequence without storing entire object in memory.
• Returns — Current length of sequence
• Args — string to append

that's the one that lets you just keep adding to your giant sequence without your RAM having a whole breakdown. we stan a memory-conscious king. 🫶

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and that's the whole page, bestie!! 🎀

perl v5.32.1 · 2021-08-15 · Bio::S...rgeSeq(3pm) — that's the version, the date, and the (truncated, as always) page name, right here in my cute little sign-off. go forth and store enormous sequences responsibly. mwah 💅✨