man arden-create (1): generate an artificial reference genome (AR) from a given input

SYNOPSIS

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

Script to generate an artificial reference genome (AR) from a given input. The AR fullfills the following conditions by default settings:

step]: has a nucleotide distribution equal to the input genome
step]: has an amino acid (aa) distribution equal to the input genome
step]: keeps the aa neighborhood similar to the neighborhood in input genome
step]: protects start and stop codons from mutations

Required Arguments:

OUTPUTFOLDER: complete path to output destination folder
INPUT FASTA: Single sequence Fasta file.

--version: show program's version number and exit
-h, --help: show this help message and exit
-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- protect ORF structure from mutations. 0 - allow mutations in start / stop codon [default: 1]
-r REVSUB, --revsub=REVSUB: 1 - reverse substitution if no suitable counterpart was found (balanced mutation). 0 - keep the unbalanced mutations.[default: 1]
-m RANDOM, --random=RANDOM: 1/0 variable. 1 - shuffled starting positions for the
: mutations. 0 - linear mutation [default: 1]
-s SORF, --saveorfs=SORF: Save found start and stop codons in a pickle file (can be loaded if the input fasta is used again if a filename is specified). [default: ]
-l LORF, --loadorfs=LORF: Specify filename to a previously created pickle file (contains positions of start/stop codons) [default: ]
-n NAME, --name=NAME: Specify name which will be used as header. [default: ]
-p PEXAMPLES, --pexamples=PEXAMPLES: set to 1 if you want to print examples