31/10/2023
This repository contains scripts relevant to submission of FunVar-tracerx manuscript and includes code-generated figures, FunVar scoring algorithm and stats calculations.
| path | Description | |
|---|---|---|
./script |
Collated scripts in submission form (ie remove hard-coded paths and any non-relevant code) | |
/fie_scoring |
Run the FunVar scoring using a flat file export[1] | |
/fie_scoring/packages |
Classes for mutations, FIEs and Grantham scoring (AAindex)[2] | |
/fie_scoring/working |
Datasets generated from FIE scoring | |
/diversity_analysis |
Hill-Shannon diversity calculations & plots | |
./data |
Datasets for figures and calculations incl db exports so can run locally | |
./plot |
Plots (except diversity) and plot data & working directory |
[1] FunVar-FIE scoring can be run interactively from:
script/fie_scoring/nfe_main.py
-
using input data (mutations, clusters, sites etc):
./data/nfe_score_database_py_funvar_archive_nfe_pfh_mutfam_090_exported_no_mut_id.tsv -
input data was generated from Oracle db by:
./data/nfe_score_database_py_export.sql
This work (excluding AAindex[2]) is licensed under a Creative Commons Attribution 4.0 International License.
[2] AAindex is provided by Kawashima et al Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database. Nucleic Acids Res. 28, 374 (2000). [PMID:10592278] https://www.genome.jp/aaindex/aaindex_help.html