diff options
Diffstat (limited to 'r_qtl')
| -rw-r--r-- | r_qtl/r_qtl2_qc.py | 12 |
1 files changed, 7 insertions, 5 deletions
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py index 43f7d94..be1eac4 100644 --- a/r_qtl/r_qtl2_qc.py +++ b/r_qtl/r_qtl2_qc.py @@ -63,12 +63,13 @@ def validate_bundle(zfile: ZipFile): "The following files do not exist in the bundle: " + ", ".join(mfile[1] for mfile in missing)) -def make_genocode_checker(genocode: dict) -> Callable[[int, str, str], Optional[InvalidValue]]: +def make_genocode_checker(genocode: dict, filename: str) -> Callable[ + [int, str, str], Optional[InvalidValue]]: """Make a checker from the genotypes in the control data""" def __checker__(lineno: int, field: str, value: str) -> Optional[InvalidValue]: genotypes = tuple(genocode.keys()) if value not in genotypes: - return InvalidValue(lineno, field, value, ( + return InvalidValue(filename, lineno, field, value, ( f"Invalid value '{value}'. Expected one of {genotypes}.")) return None return __checker__ @@ -78,14 +79,15 @@ def geno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]: cdata = rqtl2.control_data(zfile) return ( error for error in retrieve_errors( - zfile, "geno", (make_genocode_checker(cdata.get("genotypes", {})),)) + zfile, "geno", (make_genocode_checker(cdata.get("genotypes", {}), "geno"),)) if error is not None) def pheno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]: """Check for and retrieve pheno errors.""" return ( error for error in retrieve_errors( - zfile, "pheno", (partial(decimal_points_error, mini=3),)) + zfile, "pheno", (partial( + decimal_points_error, mini=3, filename="pheno"),)) if error is not None) def phenose_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]: @@ -108,7 +110,7 @@ def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) -> continue if value is not None: for checker in checkers: - yield checker(lineno, field, value) + yield checker(lineno=lineno, field=field, value=value) except rqe.MissingFileError: fname = cdata.get(filetype) yield MissingFile(filetype, fname, f"Missing '{filetype}' file '{fname}'.") |