Outputs the 0-fold and 4-fold sites from a gff and reference genome.
NOTE: Assumes there is one mutation per codon.
Requires biopython
biopython can be installed with:
pip install biopython
Usage:
python cds_fold.py -o sitefold.txt <reference.fasta> <reference.gff> > reference.log
-o with a valid file name is required. Information about failed sites is written to stdout.
usage: cds_fold.py [-h] -o OUTFILE reference gff
Generate list of 0-fold and 4-fold sites from a fasta formatted reference
genome and gff annotation file.
positional arguments:
reference Fasta formatted reference file
gff version 3 gff file.
optional arguments:
-h, --help show this help message and exit
-o OUTFILE, --outfile OUTFILE
Name of the output file
Output is tab delimited with three columns: the chromosome name, the one-indexed position, and a 0 or 4 indicating if site is 0-fold or 4-fold, respectively. For example:
#chrom pos fold
chr1 41529 0
chr1 41531 0
chr1 41533 4
chr1 41534 0