diff options
Diffstat (limited to 'scripts/run_qtlreaper.py')
| -rw-r--r-- | scripts/run_qtlreaper.py | 27 |
1 files changed, 14 insertions, 13 deletions
diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py index 89cc3ec..7d58402 100644 --- a/scripts/run_qtlreaper.py +++ b/scripts/run_qtlreaper.py @@ -6,8 +6,8 @@ import secrets import logging import subprocess from pathlib import Path -from typing import Union from functools import reduce +from typing import Union, Iterator from argparse import Namespace, ArgumentParser from gn_libs import mysqldb @@ -56,7 +56,7 @@ def reconcile_samples( def generate_qtlreaper_traits_file( outdir: Path, samples: tuple[str, ...], - traits_data: dict[str, Union[int, float]], + traits_data: tuple[dict[str, Union[int, float]], ...], filename_prefix: str = "" ) -> Path: """Generate a file for use with qtlreaper that contains the traits' data.""" @@ -65,7 +65,7 @@ def generate_qtlreaper_traits_file( _dialect.quoting=0 _traitsfile = outdir.joinpath( - f"{filename_prefix}_{secrets.token_urlsafe(15)}.tsv") + f"{filename_prefix}_{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined] with _traitsfile.open(mode="w", encoding="utf-8") as outptr: writer = csv.DictWriter( outptr, fieldnames=("Trait",) + samples, dialect=_dialect) @@ -79,7 +79,7 @@ def generate_qtlreaper_traits_file( return _traitsfile -def parse_tsv_file(results_file: Path) -> list[dict]: +def parse_tsv_file(results_file: Path) -> Iterator[dict]: """Parse the rust-qtlreaper output into usable python objects.""" with results_file.open("r", encoding="utf-8") as readptr: _dialect = csv.unix_dialect() @@ -96,7 +96,7 @@ def __qtls_by_trait__(qtls, current): } -def save_qtl_values_to_db(conn, qtls: dict): +def save_qtl_values_to_db(conn, qtls: tuple[dict, ...]): """Save computed QTLs to the database.""" with conn.cursor() as cursor: cursor.executemany( @@ -131,11 +131,11 @@ def dispatch(args: Namespace) -> int: ", ".join(_samples_not_in_genofile)) # Fetch traits data: provided list, or all traits in db - _traitsdata = phenotypes_vector_data( + _traitsdata = tuple(phenotypes_vector_data( conn, args.species_id, args.population_id, - xref_ids=tuple(args.xref_ids)).values() + xref_ids=tuple(args.xref_ids)).values()) logger.debug("Successfully got traits data. Generating the QTLReaper's traits file…") _traitsfile = generate_qtlreaper_traits_file( args.working_dir, @@ -145,7 +145,7 @@ def dispatch(args: Namespace) -> int: logger.debug("QTLReaper's Traits file: %s", _traitsfile) _qtlreaper_main_output = args.working_dir.joinpath( - f"main-output-{secrets.token_urlsafe(15)}.tsv") + f"main-output-{secrets.token_urlsafe(15)}.tsv")#type: ignore[attr-defined] logger.debug("Main output filename: %s", _qtlreaper_main_output) with subprocess.Popen( ("qtlreaper", @@ -156,11 +156,12 @@ def dispatch(args: Namespace) -> int: while _qtlreaper.poll() is None: logger.debug("QTLReaper process running…") time.sleep(1) - results = tuple(max(qtls, key=lambda qtl: qtl["LRS"]) - for qtls in - reduce(__qtls_by_trait__, - parse_tsv_file(_qtlreaper_main_output), - {}).values()) + results = tuple(#type: ignore[var-annotated] + max(qtls, key=lambda qtl: qtl["LRS"]) + for qtls in + reduce(__qtls_by_trait__, + parse_tsv_file(_qtlreaper_main_output), + {}).values()) save_qtl_values_to_db(conn, results) logger.debug("Cleaning up temporary files.") _traitsfile.unlink() |