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"""module contains code integration correlation implemented in rust here
https://github.com/Alexanderlacuna/correlation_rust
"""
import subprocess
import json
import csv
import os
from gn3.computations.qtlreaper import create_output_directory
from gn3.chancy import random_string
from gn3.settings import CORRELATION_COMMAND
from gn3.settings import TMPDIR
def generate_input_files(dataset: list[str],
output_dir: str = TMPDIR) -> tuple[str, str]:
"""function generates outputfiles and inputfiles"""
tmp_dir = f"{output_dir}/correlation"
create_output_directory(tmp_dir)
tmp_file = os.path.join(tmp_dir, f"{random_string(10)}.txt")
with open(tmp_file, "w", encoding="utf-8") as op_file:
writer = csv.writer(
op_file, delimiter=",", dialect="unix", quotechar="",
quoting=csv.QUOTE_NONE, escapechar="\\")
writer.writerows(dataset)
return (tmp_dir, tmp_file)
def generate_json_file(
tmp_dir, tmp_file, method, delimiter, x_vals) -> tuple[str, str]:
"""generating json input file required by cargo"""
tmp_json_file = os.path.join(tmp_dir, f"{random_string(10)}.json")
output_file = os.path.join(tmp_dir, f"{random_string(10)}.txt")
with open(tmp_json_file, "w", encoding="utf-8") as outputfile:
json.dump({
"method": method,
"file_path": tmp_file,
"x_vals": x_vals,
"sample_values": "bxd1",
"output_file": output_file,
"file_delimiter": delimiter
}, outputfile)
return (output_file, tmp_json_file)
def run_correlation(
dataset, trait_vals: str, method: str, delimiter: str,
corr_type: str = "sample", top_n: int = 500):
"""entry function to call rust correlation"""
# pylint: disable=too-many-arguments
(tmp_dir, tmp_file) = generate_input_files(dataset)
(output_file, json_file) = generate_json_file(
tmp_dir=tmp_dir, tmp_file=tmp_file, method=method, delimiter=delimiter,
x_vals=trait_vals)
command_list = [CORRELATION_COMMAND, json_file, TMPDIR]
try:
subprocess.run(command_list, check=True, capture_output=True)
except subprocess.CalledProcessError as cpe:
actual_command = (
os.readlink(CORRELATION_COMMAND)
if os.path.islink(CORRELATION_COMMAND)
else CORRELATION_COMMAND)
raise Exception(command_list, actual_command, cpe.stdout) from cpe
return parse_correlation_output(output_file, corr_type, top_n)
def parse_correlation_output(result_file: str,
corr_type: str, top_n: int = 500) -> dict:
"""parse file output """
# current types are sample and tissue
def __parse_line__(line):
(trait_name, corr_coeff, p_val, num_overlap) = line.rstrip().split(",")
if corr_type == "sample":
return (trait_name, {
"num_overlap": num_overlap,
"corr_coefficient": corr_coeff,
"p_value": p_val
})
if corr_type == "tissue":
return (
trait_name,
{
"tissue_corr": corr_coeff,
"tissue_number": num_overlap,
"tissue_p_val": p_val
})
return tuple(trait_name, {})
with open(result_file, "r", encoding="utf-8") as file_reader:
return dict([
__parse_line__(line)
for idx, line in enumerate(file_reader) if idx < top_n])
return {}
def get_samples(all_samples: dict[str, str],
base_samples: list[str],
excluded: list[str]):
"""filter null samples and excluded samples"""
data = {}
if base_samples:
fls = [
sm for sm in base_samples if sm not in excluded]
for sample in fls:
if sample in all_samples:
smp_val = all_samples[sample].strip()
if smp_val.lower() != "x":
data[sample] = float(smp_val)
return data
return({key: float(val.strip()) for (key, val) in all_samples.items()
if key not in excluded and val.lower().strip() != "x"})
def get_sample_corr_data(sample_type: str,
sample_data: dict[str, str],
dataset_samples: list[str]) -> dict[str, str]:
"""dependeing on the sample_type fetch the correct sample data """
if sample_type == "samples_primary":
data = get_samples(all_samples=sample_data,
base_samples=dataset_samples, excluded=[])
elif sample_type == "samples_other":
data = get_samples(
all_samples=sample_data,
base_samples=[],
excluded=dataset_samples)
else:
data = get_samples(
all_samples=sample_data, base_samples=[], excluded=[])
return data
def parse_tissue_corr_data(symbol_name: str,
symbol_dict: dict,
dataset_symbols: dict,
dataset_vals: dict):
"""parset tissue data input"""
results = None
if symbol_name and symbol_name.lower() in symbol_dict:
x_vals = [float(val) for val in symbol_dict[symbol_name.lower()]]
data = []
for (trait, symbol) in dataset_symbols.items():
try:
corr_vals = dataset_vals.get(symbol.lower())
if corr_vals:
data.append([str(trait)] + corr_vals)
except AttributeError:
pass
results = (x_vals, data)
return results
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