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

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

💖 NAME 💖

Bio::Seq::LargeSeqI — the interface class for sequences that cache their residues in a temporary file, bestie. It's giving "big sequence energy, tiny RAM budget." 🦋

✨ SYNOPSIS ✨

#

no literally that's it, that's the synopsis, the interface is that iconic 💅

🌸 DESCRIPTION 🌸

okay so. This interface class defines a whole little squad of sequence classes that do not keep their sequence info in memory — they store it in a file instead. Which means you can work with very large files even when your RAM is lowkey fighting for its life. 🫶

The most important consequence of file caching for sequences is that you do not want to inspect the sequence unless absolutely necessary. Not me being dramatic, that's just the vibe. These sequences typically override the length() method specifically so it doesn't go poking at the sequence. 👑

The seq() method is not resettable. So if you wanna add to the end of the sequence you have to use add_sequence_as_string(), and for any other sequence changes you'll have to create a new object. That's just the rules, periodt. 💀

💌 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 the Bioperl mailing list. Your participation is much appreciated. fr fr, they actually read these. ✨

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. 👑 like, the more detail the better, bestie.

🐛 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 email or the web:

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

🎀 AUTHOR - Albert Vilella 🎀

Email avilella-AT-gmail-DOT-com — main character energy, honestly 🌟

🌈 CONTRIBUTORS 🌈

Heikki Lehvaslaiho, heikki-at-bioperl-dot-org — we love a collab 💜

📖 APPENDIX 📖

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ (iykyk, that underscore means it's not for you bestie, it's an internal thing 🙈).

🌸 add_sequence_as_string

Title   : add_sequence_as_string
Usage   : $seq->add_sequence_as_string("CATGAT");
Function: Appends additional residues to an existing  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
💖 so yeah, that's the whole page. Bio::S...rgeSeqI(3pm) lives in the User Contributed Perl Documentation, and this rendering is from perl v5.32.1, dated 2021-08-15. slay, go cache some residues, ily 🫶✨🎀
📦 where this page comes from