diff options
Diffstat (limited to 'r_qtl')
| -rw-r--r-- | r_qtl/errors.py | 6 | ||||
| -rw-r--r-- | r_qtl/r_qtl2.py | 22 | ||||
| -rw-r--r-- | r_qtl/r_qtl2_qc.py | 9 |
3 files changed, 15 insertions, 22 deletions
diff --git a/r_qtl/errors.py b/r_qtl/errors.py index 20c5ced..417eb58 100644 --- a/r_qtl/errors.py +++ b/r_qtl/errors.py @@ -5,3 +5,9 @@ class RQTLError(Exception): class InvalidFormat(RQTLError): """Raised when the format of the file(s) is invalid.""" + +class MissingFileError(InvalidFormat): + """ + Raise when at least one file listed in the control file is missing from the + R/qtl2 bundle. + """ diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index c2828d2..f8c08d9 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -288,28 +288,6 @@ def sex_information(zfile: ZipFile, cdata: dict) -> Iterator[dict]: key: chain(value, partial(replace_sex_info, cdata=cdata)) for key, value in row.items() if key not in ci_fields} -def validate_bundle(zfile: ZipFile): - """Ensure the R/qtl2 bundle is valid.""" - cdata = control_data(zfile) - def __member_exists_p__(zfile, member): - if isinstance(member, str): - zfile.getinfo(member) - else: - for inner in member: - zfile.getinfo(inner) - - try: - for member in (key for key in cdata.keys() if key in __FILE_TYPES__): - __member_exists_p__(zfile, cdata[member]) - - if "file" in cdata.get("sex", {}): - __member_exists_p__(zfile, cdata["sex"]["file"]) - - if "file" in cdata.get("cross_info", {}): - __member_exists_p__(zfile, cdata["cross_info"]["file"]) - except KeyError as kerr: - raise InvalidFormat(*kerr.args) from kerr - def genotype_data(zfile: ZipFile): """Convenience function to genotype data from R/qtl2 bundle.""" cdata = control_data(zfile) diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py index f666f40..261d300 100644 --- a/r_qtl/r_qtl2_qc.py +++ b/r_qtl/r_qtl2_qc.py @@ -3,6 +3,7 @@ from zipfile import ZipFile from functools import reduce from typing import Union, Sequence +from r_qtl import errors as rqe from r_qtl import r_qtl2 as rqtl2 from r_qtl.r_qtl2 import __FILE_TYPES__ @@ -45,3 +46,11 @@ def missing_files(zfile: ZipFile) -> tuple[str]: return tuple(filter(__missing_p__, bundle_files_list(zfile, rqtl2.control_data(zfile)))) + +def validate_bundle(zfile: ZipFile): + """Ensure the R/qtl2 bundle is valid.""" + missing = missing_files(zfile) + if len(missing) > 0: + raise rqe.MissingFileError( + "The following files do not exist in the bundle: " + + ", ".join(missing)) |