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"""Procedures related gemma computations"""
import os
from base64 import b64encode
from hashlib import md5
from typing import Dict
from typing import List
from typing import ValuesView
from gn3.commands import compose_gemma_cmd
from gn3.fs_helpers import get_hash_of_files
def generate_hash_of_string(unhashed_str: str) -> str:
"""Given an UNHASHED_STRING, generate it's md5 hash while removing the '==' at
the end"""
hashed_str = md5(unhashed_str.encode("utf-8")).digest()
return b64encode(hashed_str).decode("utf-8").replace("==", "")
def generate_pheno_txt_file(trait_filename: str,
values: List,
tmpdir: str = "/tmp") -> str:
"""Given VALUES, and TMPDIR, generate a valid traits file"""
if not os.path.isdir(f"{tmpdir}/gn2/"):
os.mkdir(f"{tmpdir}/gn2/")
ext = trait_filename.partition(".")[-1]
if ext:
trait_filename = trait_filename.replace(f".{ext}", "")
ext = f".{ext}"
trait_filename += f"_{generate_hash_of_string(''.join(values))}{ext}"
# Early return if this already exists!
if os.path.isfile(f"{tmpdir}/gn2/{trait_filename}"):
return f"{tmpdir}/gn2/{trait_filename}"
with open(f"{tmpdir}/gn2/{trait_filename}", "w", encoding="utf-8") as _file:
for value in values:
if value == "x":
_file.write("NA\n")
else:
_file.write(f"{value}\n")
return f"{tmpdir}/gn2/{trait_filename}"
def do_paths_exist(paths: ValuesView) -> bool:
"""Given a list of PATHS, return False if any of them do not exist."""
for path in paths:
if not os.path.isfile(path):
return False
return True
# pylint: disable=R0913
def generate_gemma_cmd(gemma_cmd: str,
output_dir: str,
token: str,
gemma_kwargs: Dict,
gemma_wrapper_kwargs: Dict = None,
chromosomes: str = None) -> Dict:
"""Compute k values"""
_hash = get_hash_of_files(
[v for k, v in gemma_kwargs.items() if k in ["g", "p", "a", "c"]])
if chromosomes: # Only reached when calculating k-values
gemma_wrapper_kwargs = {"loco": f"{chromosomes}"}
_hash += f"-{generate_hash_of_string(chromosomes)[:6]}"
_output_filename = f"{_hash}-output.json"
return {
"output_file":
_output_filename,
"gemma_cmd":
compose_gemma_cmd(gemma_wrapper_cmd=gemma_cmd,
gemma_wrapper_kwargs=gemma_wrapper_kwargs,
gemma_kwargs=gemma_kwargs,
gemma_args=[
"-gk", ">",
(f"{output_dir}/"
f"{token}/{_output_filename}")
])
}
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