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Diffstat (limited to 'gn3/computations/qtlreaper.py')
| -rw-r--r-- | gn3/computations/qtlreaper.py | 170 |
1 files changed, 170 insertions, 0 deletions
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py new file mode 100644 index 0000000..d1ff4ac --- /dev/null +++ b/gn3/computations/qtlreaper.py @@ -0,0 +1,170 @@ +""" +This module contains functions to interact with the `qtlreaper` utility for +computation of QTLs. +""" +import os +import subprocess +from typing import Union + +from gn3.random import random_string +from gn3.settings import TMPDIR, REAPER_COMMAND + +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") 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( + 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("{}/qtlreaper".format(output_dir)) + output_filename = "{}/qtlreaper/main_output_{}.txt".format( + output_dir, random_string(10)) + output_list = ["--main_output", output_filename] + if separate_nperm_output: + permu_output_filename: Union[None, str] = "{}/qtlreaper/permu_output_{}.txt".format( + output_dir, random_string(10)) + output_list = output_list + [ + "--permu_output", permu_output_filename] # type: ignore[list-item] + else: + permu_output_filename = None + + command_list = [ + REAPER_COMMAND, "--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") 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") as infile: + lines = infile.readlines() + + return [float(line.strip()) for line in lines] |