This repository is trying to investigate differences in codon usage among various H. Sapiens populations. We are using data from 1000 Genomes Project for this purpose.
See LICENSE.
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/analyze.py – this scripts produces various statistics and statistical tests over data produced by
codon_usage.py. -
/CCDS.current.txt – Current Consensus CDS as downloaded from ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_human.
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/download_index.py – this script downloads and stores index of available whole genome samples from NCBI server and stores the result to a JSON file.
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/codon_usage.py – this script downloads whole genome CRAM file and produces codon usage statistics for each individual in an index file (see
download_index.py). -
/reference_codon_usage.json – codon usage downloaded from https://www.kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=9606 and normalized to values between 0 and 1.
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/report – final report of our findings written in LaTeX.