diff options
| -rw-r--r-- | r_qtl/r_qtl2_qc.py | 64 |
1 files changed, 39 insertions, 25 deletions
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py index 8d4fc19..4b3e184 100644 --- a/r_qtl/r_qtl2_qc.py +++ b/r_qtl/r_qtl2_qc.py @@ -2,7 +2,7 @@ import re from zipfile import ZipFile from functools import reduce -from typing import Union, Sequence, Iterator +from typing import Union, Sequence, Iterator, Optional, Callable from r_qtl import errors as rqe from r_qtl import r_qtl2 as rqtl2 @@ -59,40 +59,54 @@ def validate_bundle(zfile: ZipFile): "The following files do not exist in the bundle: " + ", ".join(missing)) +def make_genocode_checker(genocode: dict) -> 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, ( + f"Invalid value '{value}'. Expected one of {genotypes}.")) + return None + return __checker__ + def geno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]: """Check for and retrieve geno errors.""" cdata = rqtl2.control_data(zfile) - genotypes = tuple(cdata.get("genotypes", {}).keys()) - try: - for lineno, row in enumerate( - rqtl2.file_data(zfile, "geno", cdata), start=1): - for field, value in row.items(): - if field == "id": - continue - if value is not None and value not in genotypes: - yield InvalidValue(lineno, field, value, ( - f"Invalid value '{value}'. Expected one of " - f"{genotypes}.")) - except rqe.MissingFileError: - fname = cdata.get("geno") - yield MissingFile("geno", fname, f"Missing 'geno' file '{fname}'.") + return ( + error for error in retrieve_errors( + zfile, "geno", (make_genocode_checker(cdata.get("genotypes", {})),)) + if error is not None) def pheno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]: """Check for and retrieve pheno errors.""" + def __min_3_decimal_places__( + lineno: int, field: str, value: str) -> Optional[InvalidValue]: + if not (re.search(r"^([0-9]+\.[0-9]{3,}|[0-9]+\.?0*)$", value) + or re.search(r"^0\.0+$", value) + or re.search("^0+$", value)): + return InvalidValue(lineno, field, value, ( + f"Invalid value '{value}'. Expected numerical value " + "with at least 3 decimal places.")) + return None + return ( + error for error in retrieve_errors( + zfile, "pheno", (__min_3_decimal_places__,)) + if error is not None) + +def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) -> Iterator[ + Union[InvalidValue, MissingFile]]: + """Check for and retrieve errors from files of type `filetype`.""" + assert filetype in __FILE_TYPES__, f"Invalid file type {filetype}." cdata = rqtl2.control_data(zfile) try: for lineno, row in enumerate( - rqtl2.file_data(zfile, "pheno", cdata), start=1): + rqtl2.file_data(zfile, filetype, cdata), start=1): for field, value in row.items(): if field == "id": continue - if value is not None and not( - re.search(r"^([0-9]+\.[0-9]{3,}|[0-9]+\.?0*)$", value) - or re.search(r"^0\.0+$", value) - or re.search("^0+$", value)): - yield InvalidValue(lineno, field, value, ( - f"Invalid value '{value}'. Expected numerical value " - "with at least 3 decimal places.")) + if value is not None: + for checker in checkers: + yield checker(lineno, field, value) except rqe.MissingFileError: - fname = cdata.get("pheno") - yield MissingFile("pheno", fname, f"Missing 'pheno' file '{fname}'.") + fname = cdata.get(filetype) + yield MissingFile(filetype, fname, f"Missing '{filetype}' file '{fname}'.") |