Provided by: arden_1.0-4_all
arden-create - 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 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