diff options
Diffstat (limited to 'scripts/run_qtlreaper.py')
| -rw-r--r-- | scripts/run_qtlreaper.py | 20 |
1 files changed, 17 insertions, 3 deletions
diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py index ab19da0..2269ea6 100644 --- a/scripts/run_qtlreaper.py +++ b/scripts/run_qtlreaper.py @@ -6,6 +6,7 @@ import time import secrets import logging import subprocess +import multiprocessing from pathlib import Path from functools import reduce from typing import Union, Iterator @@ -147,13 +148,17 @@ def dispatch(args: Namespace) -> int: _qtlreaper_main_output = args.working_dir.joinpath( f"main-output-{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined] + _qtlreaper_permu_output = args.working_dir.joinpath( + f"permu-output-{secrets.token_urlsafe(15)}.tsv") logger.debug("Main output filename: %s", _qtlreaper_main_output) with subprocess.Popen( ("qtlreaper", "--n_permutations", "1000", "--geno", _genofile, "--traits", _traitsfile, - "--main_output", _qtlreaper_main_output), + "--main_output", _qtlreaper_main_output, + "--permu_output", _qtlreaper_permu_output, + "--threads", str(int(1+(multiprocessing.cpu_count()/2)))), env=({**os.environ, "RUST_BACKTRACE": "full"} if logger.getEffectiveLevel() == logging.DEBUG else dict(os.environ))) as _qtlreaper: @@ -172,8 +177,17 @@ def dispatch(args: Namespace) -> int: logger.debug("Cleaning up temporary files.") # short-circuits to delete file if exists - _traitsfile.exists() and _traitsfile.unlink() - _qtlreaper_main_output.exists() and _qtlreaper_main_output.unlink() + if _traitsfile.exists(): + _traitsfile.unlink() + logger.info("Deleted generated traits' file for QTLReaper.") + + if _qtlreaper_main_output.exists(): + _qtlreaper_main_output.unlink() + logger.info("Deleted QTLReaper's main output file.") + + if _qtlreaper_permu_output.exists(): + _qtlreaper_permu_output.unlink() + logger.info("Deleted QTLReaper's permutations file.") if _qtlreaper.returncode != 0: return _qtlreaper.returncode |