How to use the new project?
- Install the SierraPy project from https://github.com/hivdb/sierra-client/tree/master/python:
in short:
pip install sierrapy
- Prepare your fasta file (input.fasta) and run the following command from your command line:
sierrapy fasta input.fasta -q rega_query.gql -o input.json
where
- input.fasta is the file you just prepared
- rega_query.gql is the file created by Rega and available on the Github page (https://github.com/rega-cev/SierraPy_Rega/blob/master/rega_query.gql)
- input.json is the json result given by SierraPy
- Finally run the script parse.py (https://github.com/rega-cev/SierraPy_Rega/blob/master/parse.py) as follows:
python parse.py -i ../path/to/input.json > ../path/to/final.csv
where
- input.json is the file you got in step 2.
- final.csv will be your final resulting output csv file