Utility to generate codon mutations of a given coding DNA sequence.
usage: seq_mutations_utils.py [-h] -i INPUT_FILE -p INITIAL_POSITION
[-m MUTATIONS] -n NUM -o OUTPUT_PREFIX [-a] [-v]
[-x]
Mutations in substring
optional arguments:
-h, --help show this help message and exit
-i INPUT_FILE, --input-file INPUT_FILE
File containing the coding DNA sequence
-p INITIAL_POSITION, --initial-pos INITIAL_POSITION
Initial position of substring to modify starting from
1
-m MUTATIONS, --mutations MUTATIONS
List of mutations in the form of
'(ala,glu,...),(val,...),...' -- NOTE: the "'" must be
included
-n NUM, --num NUM Number of consecutive codons
-o OUTPUT_PREFIX, --output-prefix OUTPUT_PREFIX
Output prefix file name
-a, --all-codons Try all codons
-v, --inv Also consider combinations with original codons
without mutations
-x, --single-output-file
Create single fasta file