diff options
Diffstat (limited to 'scripts/rqtl2/phenotypes_qc.py')
| -rw-r--r-- | scripts/rqtl2/phenotypes_qc.py | 12 |
1 files changed, 12 insertions, 0 deletions
diff --git a/scripts/rqtl2/phenotypes_qc.py b/scripts/rqtl2/phenotypes_qc.py index e495a97..d565be2 100644 --- a/scripts/rqtl2/phenotypes_qc.py +++ b/scripts/rqtl2/phenotypes_qc.py @@ -3,6 +3,7 @@ import sys import tempfile from pathlib import Path from zipfile import ZipFile +from functools import reduce import multiprocessing as mproc from logging import Logger, getLogger, StreamHandler @@ -13,6 +14,8 @@ from r_qtl import r_qtl2_qc as rqc from r_qtl import exceptions as rqe from uploader.files import sha256_digest_over_file +from uploader.samples.models import samples_by_species_and_population + from scripts.rqtl2.entry import build_main from scripts.rqtl2.cli_parser import add_bundle_argument from scripts.cli_parser import init_cli_parser, add_global_data_arguments @@ -144,6 +147,15 @@ def run_qc(# pylint: disable=[too-many-arguments] ((ftype, cdata, extractiondir) for ftype in ("pheno", "phenocovar", "phenose", "phenonum"))) + # - Fetch samples/individuals from database. + samples = tuple( + item for item in set(reduce( + lambda acc, item: acc + ( + item["Name"], item["Name2"], item["Symbol"], item["Alias"]), + samples_by_species_and_population(dbconn, speciesid, populationid), + tuple())) + if bool(item)) + # - Check that `description` and `units` is present in phenocovar for # all phenotypes # - Check all phenotypes in pheno files exist in phenocovar files |