arden-create1
Generate an artificial reference genome (ar) from a given input
Usage
arden-create [options]
[OUTPUTFOLDER]
[INPUT
FASTA] ...
Overview
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
Releases
6 releases since Debian 8 (Jessie); the text changed 1 time.