BP_OLIGO_COUNT(1p)

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

bp_oligo_count 💖

okay bestie, welcome to BP_OLIGO_COUNT(1p) — yes that's the manual page name, it's giving very "I live in section 1p of the perl user-contributed docs" and honestly? iconic. let's get into it 🧚

✨ NAME ✨

bp_oligo_count — oligo count and frequency, periodt 💅

🌸 SYNOPSIS 🌸

Usage:  bp_oligo_count [-h/--help] [-l/--length OLIGOLENGTH]
        [-f/--format SEQFORMAT] [-i/--in/-s/--sequence SEQFILE]
        [-o/--out OUTFILE]

🦋 DESCRIPTION 🦋

so this script literally counts how many times every single oligonucleotide of a given length shows up, and how frequent each one is. no cap, that's the whole vibe.

why would you want that? well bestie, it's lowkey perfect for figuring out which primers are actually useful for frequent priming of nucleic acid for random labeling 👑

heads up! this script could also be run by utilizing the compseq program, which is part of EMBOSS. just so you know your options 💜

💅 OPTIONS 💅

the default sequence format is fasta, fr fr. if you don't hand over an outfile, the results just get printed to standard out, no drama. and all the other options? you can enter them interactively, main character energy 🌈

🫶 FEEDBACK 🫶

💌 Mailing Lists

user feedback is an integral part of the evolution of this and other Bioperl modules. so like, send your comments and suggestions, preferably to the Bioperl mailing list. your participation is much appreciated, and I mean that 🥺

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

🐛 Reporting Bugs

report bugs to the Bioperl bug tracking system so we can keep track of the bugs and their resolution — very organized of us, honestly. bug reports can be submitted via the web:

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

👑 AUTHOR - Charles C. Kim 👑

Email cckim@stanford.edu 💖

⭐ HISTORY ⭐

  • Written July 2, 2001 📅
  • Submitted to bioperl scripts project 2001/08/06
  • >> 100 x speed optimization by Heikki Lehvaslaiho 🔥 (not me being obsessed with a 100x speedup, that's actually slay)

and that's the whole page bestie! this one shipped with perl v5.32.1 and it's dated 2021-08-15 — mwah, go count some oligos 🎀💜

📦 where this page comes from