Build the package
Build the package with Nimble (included with Nim). The tool takes care of dependencies:
$ nimble build covidphy_cli
Using the CLI
Classify a fasta sequence into haplogroups, returning a Json representation.
Usage:
covidphy_cli --fasta:path/to/file.fas
covidphy_cli --f:path/to/file.fas
cat path/to/file.fas | covidphy_cli
Options:
-h --help Show this message.
-v --version Show the version.
-f --fasta The path to the fasta file. Only the first sequence of the
file is going to be used.
A Json is returned, with the following schema:
{"haplogroups": [
{"name":"A",
"pathway":[]}
],
"variants": ["T2C"...],
"length":29757}