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"""Procedures related rqtl computations"""
from typing import Dict
from gn3.commands import compose_rqtl_cmd
from gn3.computations.gemma import generate_hash_of_string
from gn3.fs_helpers import get_hash_of_files
def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
rqtl_wrapper_kwargs: Dict,
rqtl_wrapper_bool_kwargs: list) -> Dict:
"""Given the base rqtl_wrapper command and
dict of keyword arguments, return the full rqtl_wrapper command and an
output filename generated from a hash of the genotype and phenotype files
"""
# Generate a hash from contents of the genotype and phenotype files
_hash = get_hash_of_files(
[v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]])
# Append to hash a hash of keyword arguments
_hash += generate_hash_of_string(
",".join([f"{k}:{v}" for k, v in rqtl_wrapper_kwargs.items() if k not in ["g", "p"]]))
# Append to hash a hash of boolean keyword arguments
_hash += generate_hash_of_string(
",".join(rqtl_wrapper_bool_kwargs))
# Temporarily substitute forward-slashes in hash with underscores
_hash = _hash.replace("/", "_")
_output_filename = f"{_hash}-output.json"
return {
"output_file":
_output_filename,
"rqtl_cmd":
compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
rqtl_wrapper_kwargs=rqtl_wrapper_kwargs,
rqtl_wrapper_bool_kwargs=rqtl_wrapper_bool_kwargs)
}
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