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"""
This module contains functions to interact with the `qtlreaper` utility for
computation of QTLs.
"""
import os
import subprocess
from typing import Union
from gn3.chancy import random_string
from gn3.settings import TMPDIR
def generate_traits_file(samples, trait_values, traits_filename):
"""
Generate a traits file for use with `qtlreaper`.
PARAMETERS:
samples: A list of samples to use as the headers for the various columns.
trait_values: A list of lists of values for each trait and sample.
traits_filename: The tab-separated value to put the values in for
computation of QTLs.
"""
header = "Trait\t{}\n".format("\t".join(samples))
data = (
[header] +
["{}\t{}\n".format(i+1, "\t".join([str(i) for i in t]))
for i, t in enumerate(trait_values[:-1])] +
["{}\t{}".format(
len(trait_values), "\t".join([str(i) for i in t]))
for t in trait_values[-1:]])
with open(traits_filename, "w", encoding="utf8") as outfile:
outfile.writelines(data)
def create_output_directory(path: str):
"""Create the output directory at `path` if it does not exist."""
try:
os.mkdir(path)
except FileExistsError:
# If the directory already exists, do nothing.
pass
def run_reaper(
reaper_cmd: str,
genotype_filename: str, traits_filename: str,
other_options: tuple = ("--n_permutations", "1000"),
separate_nperm_output: bool = False,
output_dir: str = TMPDIR):
"""
Run the QTLReaper command to compute the QTLs.
PARAMETERS:
genotype_filename: The complete path to a genotype file to use in the QTL
computation.
traits_filename: A path to a file previously generated with the
`generate_traits_file` function in this module, to be used in the QTL
computation.
other_options: Other options to pass to the `qtlreaper` command to modify
the QTL computations.
separate_nperm_output: A flag indicating whether or not to provide a
separate output for the permutations computation. The default is False,
which means by default, no separate output file is created.
output_dir: A path to the directory where the outputs are put
RETURNS:
The function returns a tuple of the main output file, and the output file
for the permutation computations. If the `separate_nperm_output` is `False`,
the second value in the tuple returned is `None`.
RAISES:
The function will raise a `subprocess.CalledProcessError` exception in case
of any errors running the `qtlreaper` command.
"""
create_output_directory(f"{output_dir}/qtlreaper")
output_filename = (
f"{output_dir}/qtlreaper/main_output_{random_string(10)}.txt")
output_list = ["--main_output", output_filename]
if separate_nperm_output:
permu_output_filename: Union[None, str] = (
f"{output_dir}/qtlreaper/permu_output_{random_string(10)}.txt")
output_list = output_list + [
"--permu_output", permu_output_filename] # type: ignore[list-item]
else:
permu_output_filename = None
command_list = [
reaper_cmd, "--geno", genotype_filename,
*other_options, # this splices the `other_options` list here
"--traits", traits_filename,
*output_list # this splices the `output_list` list here
]
subprocess.run(command_list, check=True)
return (output_filename, permu_output_filename)
def chromosome_sorter_key_fn(val):
"""
Useful for sorting the chromosomes
"""
if isinstance(val, int):
return val
return ord(val)
def organise_reaper_main_results(parsed_results):
"""
Provide the results of running reaper in a format that is easier to use.
"""
def __organise_by_chromosome(chr_name, items):
chr_items = [item for item in items if item["Chr"] == chr_name]
return {
"Chr": chr_name,
"loci": [{
"Locus": locus["Locus"],
"cM": locus["cM"],
"Mb": locus["Mb"],
"LRS": locus["LRS"],
"Additive": locus["Additive"],
"pValue": locus["pValue"]
} for locus in chr_items]}
def __organise_by_id(identifier, items):
id_items = [item for item in items if item["ID"] == identifier]
unique_chromosomes = {item["Chr"] for item in id_items}
return {
"ID": identifier,
"chromosomes": {
_chr["Chr"]: _chr for _chr in [
__organise_by_chromosome(chromo, id_items)
for chromo in sorted(
unique_chromosomes, key=chromosome_sorter_key_fn)]}}
unique_ids = {res["ID"] for res in parsed_results}
return {
trait["ID"]: trait for trait in
[__organise_by_id(_id, parsed_results) for _id in sorted(unique_ids)]}
def parse_reaper_main_results(results_file):
"""
Parse the results file of running QTLReaper into a list of dicts.
"""
with open(results_file, "r", encoding="utf8") as infile:
lines = infile.readlines()
def __parse_column_float_value(value):
# pylint: disable=W0702
try:
return float(value)
except:
return value
def __parse_column_int_value(value):
# pylint: disable=W0702
try:
return int(value)
except:
return value
def __parse_line(line):
items = line.strip().split("\t")
return items[0:2] + [__parse_column_int_value(items[2])] + [
__parse_column_float_value(item) for item in items[3:]]
header = lines[0].strip().split("\t")
return [dict(zip(header, __parse_line(line))) for line in lines[1:]]
def parse_reaper_permutation_results(results_file):
"""
Parse the results QTLReaper permutations into a list of values.
"""
with open(results_file, "r", encoding="utf8") as infile:
lines = infile.readlines()
return [float(line.strip()) for line in lines]
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