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| author | Frederick Muriuki Muriithi | 2024-02-21 09:19:24 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2024-02-21 09:19:24 +0300 |
| commit | 6462099372626e11706219a695e8303250359510 (patch) | |
| tree | 33be5ad00867bcb4c9ca5b4ee112de8803d8c49b /scripts | |
| parent | ce243a57b24d6adecb169487e706290d91b22d19 (diff) | |
| download | gn-uploader-6462099372626e11706219a695e8303250359510.tar.gz | |
Pass 'filename' value to error checker function.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/qc_on_rqtl2_bundle.py | 9 |
1 files changed, 5 insertions, 4 deletions
diff --git a/scripts/qc_on_rqtl2_bundle.py b/scripts/qc_on_rqtl2_bundle.py index 027f387..37b8a9e 100644 --- a/scripts/qc_on_rqtl2_bundle.py +++ b/scripts/qc_on_rqtl2_bundle.py @@ -97,7 +97,7 @@ def retrieve_errors_with_progress(rconn: Redis,#pylint: disable=[too-many-locals continue if value is not None: for checker in checkers: - error = checker(lineno, field, value) + error = checker(lineno=lineno, field=field, value=value) if bool(error): yield error __update_processed__(value) @@ -133,9 +133,10 @@ def qc_pheno_errors(rconn, fqjobid, zfile, logger) -> bool: cdata = rqtl2.control_data(zfile) if "pheno" in cdata: logger.info("Checking for errors in the 'pheno' file…") - perrs = tuple(retrieve_errors_with_progress( - rconn,fqjobid, zfile, "pheno", - (partial(decimal_points_error, mini=3),))) + perrs = check_pheno_samples(zfile.filename, logger) + tuple( + retrieve_errors_with_progress( + rconn,fqjobid, zfile, "pheno", + (partial(decimal_points_error, filename="pheno", mini=3),))) add_to_errors(rconn, fqjobid, "errors-generic", tuple( err for err in perrs if isinstance(err, rqfe.MissingFile))) add_to_errors(rconn, fqjobid, "errors-pheno", tuple( |