NOTE: Please consider using degenotate instead.
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
This code was first used in The population genetics of convergent adaptation in maize and teosinte is not locally re Population Genetics of Convergent Adaptation in Maize and Teosinte is Not Locally Restricted, and can be cited if this software is used in your own work.