diff options
Diffstat (limited to 'r_qtl')
| -rw-r--r-- | r_qtl/r_qtl2.py | 4 | ||||
| -rw-r--r-- | r_qtl/r_qtl2_qc.py | 18 |
2 files changed, 19 insertions, 3 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index f8c08d9..e74312f 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -10,7 +10,7 @@ import yaml from functional_tools import take, chain -from r_qtl.errors import InvalidFormat +from r_qtl.errors import InvalidFormat, MissingFileError __FILE_TYPES__ = ( "geno", "founder_geno", "pheno", "covar", "phenocovar", "gmap", "pmap", @@ -250,7 +250,7 @@ def file_data(zfile: ZipFile, zfile, member_key, cdata, process_transposed_value): yield row except KeyError as exc: - raise InvalidFormat(*exc.args) from exc + raise MissingFileError(*exc.args) from exc def cross_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: """Load cross information where present.""" diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py index 853c34b..70a00f9 100644 --- a/r_qtl/r_qtl2_qc.py +++ b/r_qtl/r_qtl2_qc.py @@ -1,7 +1,7 @@ """Quality control checks for R/qtl2 data bundles.""" from zipfile import ZipFile from functools import reduce -from typing import Union, Sequence +from typing import Union, Sequence, Iterator, Optional from r_qtl import errors as rqe from r_qtl import r_qtl2 as rqtl2 @@ -54,3 +54,19 @@ def validate_bundle(zfile: ZipFile): raise rqe.MissingFileError( "The following files do not exist in the bundle: " + ", ".join(missing)) + +def geno_errors(zfile: ZipFile) -> Iterator[tuple[Optional[int], Optional[str], str]]: + """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 (lineno, field, ( + f"Invalid value '{value}'. Expected one of {genotypes}")) + except rqe.MissingFileError: + yield (None, None, "Missing 'geno' file.") |