https://github.com/poeli/cov_tracker
EDGE COVID19 variant tracking
https://github.com/poeli/cov_tracker
Last synced: 4 months ago
JSON representation
EDGE COVID19 variant tracking
- Host: GitHub
- URL: https://github.com/poeli/cov_tracker
- Owner: poeli
- License: gpl-3.0
- Created: 2021-08-24T19:49:15.000Z (about 4 years ago)
- Default Branch: main
- Last Pushed: 2022-08-01T13:32:26.000Z (about 3 years ago)
- Last Synced: 2025-03-30T00:24:40.925Z (6 months ago)
- Language: HTML
- Size: 8.38 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# SARS-CoV-2 variant tracking
## Installation
```
pip install -r requirements.txt
python setup.py install
```
## Test
```
# convert GISAID metadata.tsv file to .pkl files (metadata.pkl and metadata.mutation.pkl)
ec19_varviz tsv2pkl \
--tsv /path/to/gisaid/metadata.tsv \
--prefix test/metadata
# generate global stats
ec19_varviz gisaid_stats \
--meta-pkl test/metadata.pkl \
--mut-pkl test/metadata.mutation.pkl \
--output test/metadata_global.html
# generate US stats and display lineage distributions for each state
ec19_varviz gisaid_stats \
--meta-pkl test/metadata.pkl \
--mut-pkl test/metadata.mutation.pkl \
--geo-type country \
--country USA \
--output test/metadata_USA.html
# generate California stats and display lineage distributions for each county
ec19_varviz gisaid_stats \
--meta-pkl test/metadata.pkl \
--mut-pkl test/metadata.mutation.pkl \
--geo-type state \
--country USA \
--state California \
--output test/metadata_CA.html
# generate lineage tracking info for an EC19 project (USA only)
ec19_varviz project \
--meta-pkl test/metadata.pkl \
--mut-pkl test/metadata.mutation.pkl \
--sample 2251_127 \
--snps test/NC_045512.2_consensus.SNPs_report.txt \
--pango test/NC_045512.2_consensus_lineage.txt \
--metadata test/metadata_gisaid_ncbi.txt \
--geo-type country \
--country USA \
--output test/ec19_project_2251_127.html
# generate report for EC19 projects
ec19_varviz report \
--snps test/lanl_project_list.SNP.tsv \
--gaps test/lanl_project_list.gaps.tsv \
--alnstats test/lanl_project_list.alnstats.tsv \
--pango test/lanl_project_list.lineage_report.csv \
--metadata test/lanl_project_list.metadata.tsv \
--output test/lanl_project_list_ec19.html
```