NAME

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

SYNOPSIS

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

DESCRIPTION

       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

OPTIONS

       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

arden-create 2013-04-25                           February 2014                                  ARDEN-CREATE(1)