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"""Procedures used to work with the various bio-informatics cli
commands"""
from typing import Dict
from typing import List
from typing import Optional
from gn3.file_utils import lookup_file
from gn3.file_utils import jsonfile_to_dict
# pylint: disable=locally-disabled, too-many-arguments
def compose_gemma_cmd(
token: str,
metadata_filename: str,
gemma_wrapper_cmd: str = "gemma-wrapper",
gemma_wrapper_kwargs: Optional[Dict] = None,
gemma_kwargs: Optional[Dict] = None,
gemma_args: Optional[List] = None) -> str:
"""Compose a valid GEMMA command given the correct values"""
cmd = f"{gemma_wrapper_cmd} --json"
if gemma_wrapper_kwargs:
cmd += (" " # Add extra space between commands
" ".join([f" --{key} {val}" for key, val
in gemma_wrapper_kwargs.items()]))
data = jsonfile_to_dict(lookup_file("TMPDIR",
token,
metadata_filename))
geno_file = lookup_file(environ_var="TMPDIR",
root_dir="genotype",
file_name=data.get("geno", ""))
pheno_file = lookup_file(environ_var="TMPDIR",
root_dir=token,
file_name=data.get("geno", ""))
cmd += f" -- -g {geno_file} -p {pheno_file}"
if gemma_kwargs:
cmd += (" "
" ".join([f" -{key} {val}"
for key, val in gemma_kwargs.items()]))
if gemma_args:
cmd += (" "
" ".join([f" {arg}" for arg in gemma_args]))
return cmd
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