aboutsummaryrefslogtreecommitdiff
path: root/r_qtl
diff options
context:
space:
mode:
Diffstat (limited to 'r_qtl')
-rw-r--r--r_qtl/r_qtl2_qc.py16
1 files changed, 8 insertions, 8 deletions
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
index 261d300..853c34b 100644
--- a/r_qtl/r_qtl2_qc.py
+++ b/r_qtl/r_qtl2_qc.py
@@ -7,23 +7,23 @@ from r_qtl import errors as rqe
from r_qtl import r_qtl2 as rqtl2
from r_qtl.r_qtl2 import __FILE_TYPES__
-def bundle_files_list(zfile, cdata: dict) -> tuple[str]:
+def bundle_files_list(cdata: dict) -> tuple[str, ...]:
"""Retrieve files listed in control file."""
def __merge__(alist: tuple[str, ...], member: Union[str, Sequence[str]]) -> tuple[str, ...]:
if isinstance(cdata[member], str):
return alist + (cdata[member],)
return alist + tuple(cdata[member])
- fileslist = tuple()
- fileslist = reduce(__merge__,
- (key for key in cdata.keys() if key in __FILE_TYPES__),
- tuple())
+ fileslist: tuple[str, ...] = reduce(
+ __merge__,
+ (key for key in cdata.keys() if key in __FILE_TYPES__),
+ tuple())
if "file" in cdata.get("sex", {}):
sexfile = cdata["sex"]["file"]
fileslist = fileslist + (
(sexfile,) if isinstance(sexfile, str) else tuple(sexfile))
-
+
if "file" in cdata.get("cross_info", {}):
crossinfofile = cdata["cross_info"]["file"]
fileslist = fileslist + (
@@ -32,7 +32,7 @@ def bundle_files_list(zfile, cdata: dict) -> tuple[str]:
return fileslist
-def missing_files(zfile: ZipFile) -> tuple[str]:
+def missing_files(zfile: ZipFile) -> tuple[str, ...]:
"""
Retrieve a list of files listed in the control file that do not exist in the
bundle.
@@ -45,7 +45,7 @@ def missing_files(zfile: ZipFile) -> tuple[str]:
return True
return tuple(filter(__missing_p__,
- bundle_files_list(zfile, rqtl2.control_data(zfile))))
+ bundle_files_list(rqtl2.control_data(zfile))))
def validate_bundle(zfile: ZipFile):
"""Ensure the R/qtl2 bundle is valid."""