Man page - arden-create(1)

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Package: arden
apt-get install arden

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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