ARDEN-CREATE(1)

💖 ARDEN-CREATE — the manual, but make it cute 💖

okay bestie, welcome to arden-create(1), a User Commands classic ✨ she's a script, she's iconic, and she's about to build you an artificial reference genome (aka an AR) out of whatever input you hand her. no cap. let's get into it 🧚

🌸 NAME 🌸

arden-create — generate an artificial reference genome (AR) from a given input 🦋

✨ SYNOPSIS ✨

arden-create [options] [OUTPUTFOLDER] [INPUT FASTA]...

👑 DESCRIPTION 👑

so the whole vibe is: this script generates an artificial reference genome (an AR) from an input you give it. and like, by default settings, the AR fulfills these conditions — like, all of them, she's an overachiever 💅:

1. has a nucleotide distribution equal to the input genome
2. has an amino acid (aa) distribution equal to the input genome
3. keeps the aa neighborhood similar to the neighborhood in input genome
4. protects start and stop codons from mutations

periodt. she's giving main character energy fr fr 🌟

🎀 OPTIONS 🎀

🍓 Required Arguments (yes, you literally have to give her these)

• OUTPUTFOLDER — the complete path to the output destination folder 📁 like, the whole path, not a vibe, an actual path.
• INPUT FASTA — a single sequence Fasta file. one sequence. just one. single. 🫶

🌈 The Rest Of The Options

• --version — show the program's version number and dip out ✌️
• -h, --help — show this help message and exit. your girl is helpful 💁
• -d DISTANCE, --distance=DISTANCE — distance between 2 mutations on DNA level. the minimum distance will then be d-3. [default: 15] 📏
• -o ORF, --orf=ORF — 1 protects the ORF structure from mutations; 0 allows mutations in the start / stop codon. [default: 1] 🛡️
• -r REVSUB, --revsub=REVSUB — 1 reverses the substitution if no suitable counterpart was found (balanced mutation); 0 keeps the unbalanced mutations. [default: 1] 🔄
• -m RANDOM, --random=RANDOM — a 1/0 variable. 1 means shuffled starting positions for the mutations; 0 means linear mutation. [default: 1] 🎲
• -s SORF, --saveorfs=SORF — save the found start and stop codons into a pickle file. you can load it later if you use the same input fasta again — but only if a filename is specified. [default: `] 🥒
• -l LORF, --loadorfs=LORF — specify a filename pointing to a previously created pickle file (it contains the positions of the start/stop codons). [default: `] 📂
• -n NAME, --name=NAME — specify the name that will be used as the header. [default: `] 🏷️
• -p PEXAMPLES, --pexamples=PEXAMPLES — set this to 1 if you want her to print examples. [no default listed — you decide bestie] 🖨️

heads up bestie: those defaults with nothing after them (-s, -l, -n) are literally empty by default — nothing is filled in until you say so. no assumptions here, iykyk 🙈

💜 A lil sign-off 💜

this page is arden-create 2013-04-25 energy, dated February 2014, and it lives in the ARDEN-CREATE(1) manual section. love that for her. she ate and left no crumbs 🍽️✨ bye bestie, go build a genome 💖🦋🌸