BP_GCCALC(1)

📦 version 1.7.8, in nixos 26.05, nixpkgs unstable

💅 BP_GCCALC(1) — like, the gc calculator era 💅

okay so this is one of those User Contributed Perl Documentation pages (that's the manual name bestie, i'm folding it in right here at the top so you're not confused later) and it's about a script called bp_gccalc. it's not a huge page, but it ate, and we're gonna go through every single bit of it. no skipping. 🫶

✨ NAME ✨

bp_gccalc — literally just: the GC content of nucleotide sequences. that's the whole vibe. 🧬💖

✨ SYNOPSIS ✨

three whole ways to run it, and honestly? all iconic. look:

  bp_gccalc [-f/--format FORMAT] [-h/--help] filename
  or
  bp_gccalc [-f/--format FORMAT] < filename
  or
  bp_gccalc [-f/--format FORMAT] -i filename

the ors are doing a lot of work there. read them. they matter. 😌

✨ DESCRIPTION ✨

okay so what does this thing actually do? this script prints out the GC content for every nucleotide sequence from the input file. every single one. it's giving thorough. it's giving main character energy. 🔥

✨ OPTIONS ✨

first things first, the default sequence format is fasta. no cap. that's the default, that's what you get if you don't say otherwise. 🌸

and here's the part you actually need — the sequence input can be provided using any of the three methods. pick your fighter:

  • unnamed argument — just yeet the filename on there, like this:
  bp_gccalc filename
  • named argument — when you wanna be all formal and specify it with -i:
  bp_gccalc -i filename
  • standard input — classic pipes-and-stdin moment, lowkey the coolest one:
  bp_gccalc < filename

all three ways? valid. slay. 💅

✨ FEEDBACK ✨

Mailing Lists 🎀

user feedback is an integral part of the evolution of this and other Bioperl modules — and like, that's not just a nice-sounding line, it's genuinely true. send your comments and suggestions preferably to the Bioperl mailing list. your participation is much appreciated. 💖

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

Reporting Bugs 🦋

found a bug? no stress bestie, report it to the Bioperl bug tracking system — it helps them keep track of the bugs and their resolution. genuinely useful. bug reports can be submitted via the web:

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

✨ AUTHOR - Jason Stajich ✨

the person behind it. the icon. the moment. 👑

Email jason@bioperl.org

✨ HISTORY ✨

a little lore for you, because we love context:

  • based on script code (see bottom) submitted by cckim@stanford.edu
  • submitted as part of bioperl script project 2001/08/06

ngl, 2001/08/06 is such an old date and yet here we are, still calculating GC content. 🫡

and that's the whole page! no filler, no fear. this was brought to you by perl v5.42.3, dated 2021-02-03 — so go forth, plug in your fasta, and let bp_gccalc tell you your GC content ✨💜🍓

📦 where this page comes from