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arden-create - Online in the Cloud

Run arden-create in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command arden-create that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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
fullfills 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

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