C-SIBELIA.PY(1)

📦 version 3.0.7, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 C-SIBELIA.PY(1) 💖

okay so this page lives in the User Commands manual 🎀 bestie, let's get into it ✨

🧚 NAME

C-Sibelia.py - comparing two microbial genomes 🦋

💅 DESCRIPTION

the way the usage line looks like a whole puzzle 😭 here's how it's laid out:

usage: C-Sibelia.py [-h] [-s PARAMETERS] [-m MINBLOCKSIZE] [-p
PROCESSCOUNT]

[-i MAXITERATIONS] [--maf MAF] [-v VARIANT] [-u UNMAPPED]
       [--debug] [-t TEMPDIR | -o OUTDIR] reference assembly

so C-Sibelia.py is a tool for comparing two microbial genomes, and it's literally iconic for that 🔥

positional arguments

these two are required, no skipping them 🫶

  • reference — a multi-FASTA file with the reference genome 🌸
  • assembly — a multi-FASTA file with the assembly genome 🌸

optional arguments

the fun part 🧁 these are all the flags you can toss in:

  • -h, --help — shows the help message and exits 💀
  • -s PARAMETERS, --parameters PARAMETERS — sets the parameter set used for simplification. loose gives you fewer blocks but they're chunkier, and fine is the total opposite 🧚 (default: fine)
  • -m MINBLOCKSIZE, --minblocksize MINBLOCKSIZE — the minimum size of a synteny block 📏 (default: 500)
  • -p PROCESSCOUNT, --processcount PROCESSCOUNT — how many processes run at once 🏃‍♀️ (default: 1)
  • -i MAXITERATIONS, --maxiterations MAXITERATIONS — the max number of iterations during one stage of simplification 🔁 (default: 4)
  • --maf MAF — an output file for storing alignments in MAF format 📁 (default: None)
  • -v VARIANT, --variant VARIANT — an output file with the detected variants 🦋 (default: variant.vcf)
  • -u UNMAPPED, --unmapped UNMAPPED — an output file for storing unmapped insertions in text format 📝 (default: None)
  • --debug — generates output in text files 🙈 (default: False)
  • -t TEMPDIR, --tempdir TEMPDIR — a directory for temporary files 🗂️ (default: None)
  • -o OUTDIR, --outdir OUTDIR — a directory for synteny block output files 💜 (default: None)
the usage line shows -t and -o as an either/or pick, so you choose one 💅

🎀 AUTHOR

this manpage was written by Andreas Tille for the Debian distribution, and it's totally free to use for any other usage of the program 🌈

that's the tea 🍓 C-Sibelia.py version 3.0.7+ds, February 2019, and this page is fully iconic in the User Commands manual 👑 stay hydrated, bestie 🫶✨

📦 where this page comes from