arden-create

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

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

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

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