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

💖 Bio::S...marySeq 💖

okay bestie, so this is the perl doc for Bio::Seq::LargePrimarySeq — it lives in the Bio::S...marySeq(3pm) man page, and it's a PrimarySeq object that stores sequence as files in the tempdir (as found by File::Temp) or the default method in Bio::Root::Root. big-seq energy, no memory meltdown, we love to see it 🫶

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✨ SYNOPSIS ✨

  # normal primary seq usage

that's it. that's the synopsis. iconic minimalism 💅

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🌸 DESCRIPTION 🌸

so this object stores a sequence as a series of files in a temporary directory. the whole point? letting you hold very large sequences (like, > 100MBases big) on a file system without running out of memory — yes, even on a 64 MB real memory machine. imagine. we're thriving 🦋

of course, to actually make use of this functionality, the programs using this object must not call $primary_seq->seq — otherwise the entire sequence comes out into memory and probably pastes your machine 💀 (fr fr, it's giving catastrophic). BUT. calls like $primary_seq->subseq(10,100) will only bring 90 characters into real memory. slay. small, contained, respectful of your RAM 👑

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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. the more detail the better, bestie, don't be shy 🎀

🐛 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

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👑 AUTHOR - Ewan Birney, Jason Stajich 👑

Email birney@ebi.ac.uk Email jason@bioperl.org

two absolute legends, we stan 🌟

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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 backstage pass only 🙈)

⭐ length

• Title : length
• Usage :
• Function :
• Example :
• Returns :
• Args :

(no notes, no drama, just vibes ✨)

⭐ seq

• Title : seq
• Usage :
• Function :
• Example :
• Returns :
• Args :

⭐ subseq

• Title : subseq
• Usage :
• Function :
• Example :
• Returns :
• Args :

⭐ 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

okay this one is the moment. you're building your huge sequence piece by piece and never storing the whole thing in memory. main character energy 🔥

⭐ _filename

• Title : _filename
• Usage : $obj->_filename($newval)
• Function :
• Example :
• Returns : value of _filename
• Args : newvalue (optional)

⭐ alphabet

• Title : alphabet
• Usage : $obj->alphabet($newval)
• Function :
• Example :
• Returns : value of alphabet
• Args : newvalue (optional)

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and that's the whole page, bestie!! every flag, every method, every email, nothing skipped, no cap 💖

this whole thing was served to you by perl v5.32.1, dated 2021-08-15, in the Bio::S...marySeq(3pm) man page. periodt. go forth and store ur giant sequences responsibly 🌈💜