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

ARDEN-CREATE(1) User Commands ARDEN-CREATE(1)

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
0[step]
has an amino acid (aa) distribution equal to the input genome
0[step]
keeps the aa neighborhood similar to the neighborhood in input genome
0[step]
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
February 2014 arden-create 2013-04-25