Generate an artificial reference genome (ar) from a given input
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:
has a nucleotide distribution equal to the input genome
has an amino acid (aa) distribution equal to the input genome
keeps the aa neighborhood similar to the neighborhood in input genome
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