Get report for each query mutation from outbreak.info resource and find out in which lineages this mutation is present and at what abudance. The output is a tab-delimited file for each query.
The script queries outbreak.info and stores cached data. The maximum age of cached file is 24hrs after which a fresh data snapshot is downloaded
- python 3
- requests >= 2.0
Minimum requirements are needed to run this script. To quickly install all necessary libraries run pip install -r requirements.txt
Simply run as any Python script by specifying mutation in the following formats: a) for substitution : (s:n501y); b) deletions :(s:del69/70 or orf1a:del17)
usage: outbreakinfointerrogator.py uses https://api.outbreak.info/
to get information on query mutations supported by GISAID database data
optional arguments:
-h, --help show this help message and exit
-m MUTATION_NAME, --mutation_name MUTATION_NAME
Mutation name to query (e.g. s:del69/70, s:d614g,orf1a:del17)
| Mutation | #PangoLineages | PangoNames(prevalence in lineage) |
|---|---|---|
| s:d614g | 1196 | A.18(1.0),A.19(1.0),B.1.1.3(1.0),B.1.1.4(1.0) |