diff options
Diffstat (limited to 'r_qtl/r_qtl2_qc.py')
| -rw-r--r-- | r_qtl/r_qtl2_qc.py | 26 |
1 files changed, 4 insertions, 22 deletions
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py index f62f142..aa5c81e 100644 --- a/r_qtl/r_qtl2_qc.py +++ b/r_qtl/r_qtl2_qc.py @@ -1,7 +1,6 @@ """Quality control checks for R/qtl2 data bundles.""" -import re from zipfile import ZipFile -from functools import reduce +from functools import reduce, partial from typing import Union, Iterator, Optional, Callable from r_qtl import errors as rqe @@ -10,6 +9,7 @@ from r_qtl.r_qtl2 import __FILE_TYPES__ from r_qtl.fileerrors import MissingFile from quality_control.errors import InvalidValue +from quality_control.checks import decimal_points_error def bundle_files_list(cdata: dict) -> tuple[tuple[str, str], ...]: """Retrieve files listed in control file.""" @@ -83,34 +83,16 @@ def geno_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]: 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+$", value)): - return InvalidValue(lineno, field, value, ( - f"Invalid value '{value}'. Expected numerical value " - "with at least 3 decimal places.")) - return None return ( error for error in retrieve_errors( - zfile, "pheno", (__min_3_decimal_places__,)) + zfile, "pheno", (partial(decimal_points_error, mini=3),)) if error is not None) def phenose_errors(zfile: ZipFile) -> Iterator[Union[InvalidValue, MissingFile]]: """Check for and retrieve phenose errors.""" - def __min_6_decimal_places__( - lineno: int, field: str, value: str) -> Optional[InvalidValue]: - if not (re.search(r"^([0-9]+\.[0-9]{6,}|[0-9]+\.?0*)$", 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 6 decimal places.")) - return None return ( error for error in retrieve_errors( - zfile, "phenose", (__min_6_decimal_places__,)) + zfile, "phenose", (partial(decimal_points_error, mini=6),)) if error is not None) def retrieve_errors(zfile: ZipFile, filetype: str, checkers: tuple[Callable]) -> Iterator[ |