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Installation
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Create your virtual environment
python3.9 -m virtualenv venv -
Activate your virtual environment
source venv/bin/activate -
Follow the instructions at https://github.com/veg/hivtrace for installation
pip3 install biopython
pip3 install numpy==1.20
pip3 install scipy
pip3 install cython
pip3 install hivtrace
- Ensure
tn93is installed
git clone https://github.com/veg/tn93.git
cd tn93
cmake .
make
make install (optional)
- Run HIV-TRACE with Dummy Dataset HIV-TRACE currently only anticipates a FASTA file. A dataset used in an analysis in 2019 is available at https://github.com/veg/kpnet-global/blob/master/data/kp-aligned.fas.
The site range we are using for this example is
- Sites : 2253-3869
- Minimum Length : 500
hivtrace -i ./sequence.fasta -t 0.015 -r /Directory/to/hivtrace/hivtrace/test/rsrc/HXB2_1497.fasta -a resolve -m 500 -g 0.015
Documentation for hivtrace is located at https://github.com/veg/hivtrace.
- Annotate the results file (optional)
Attributes for the dataset we used is available at https://github.com/veg/kpnet-global/blob/master/data/kp-data.tsv.
hivnetworkannotate -n sequence.fasta.results.json -a attributes.json -g schema.json -r
Some documentation for for hivnetworkannotate exists at https://github.com/veg/hivclustering/wiki/hivnetworkannotate. I prefer to use JSON with hivnetworkannotate, as the command is more approachable. In order to translate an attributes tsv to JSON, you can use the following deno script. https://github.com/stevenweaver/autotune-app/blob/main/scripts/deno/tsv2json.ts
To generate a schema from the attributes, you can use https://github.com/stevenweaver/autotune-app/blob/main/scripts/deno/generateSchema.ts.
- Visualize the results
By navigating to https://veg.github.io/hivtrace-viz/, you can select your results file to view by clicking on File > Load.