aboutsummaryrefslogtreecommitdiff
path: root/r_qtl
diff options
context:
space:
mode:
Diffstat (limited to 'r_qtl')
-rw-r--r--r_qtl/r_qtl2_qc.py47
1 files changed, 47 insertions, 0 deletions
diff --git a/r_qtl/r_qtl2_qc.py b/r_qtl/r_qtl2_qc.py
new file mode 100644
index 0000000..f666f40
--- /dev/null
+++ b/r_qtl/r_qtl2_qc.py
@@ -0,0 +1,47 @@
+"""Quality control checks for R/qtl2 data bundles."""
+from zipfile import ZipFile
+from functools import reduce
+from typing import Union, Sequence
+
+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]:
+ """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())
+
+ 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 + (
+ (crossinfofile,) if isinstance(crossinfofile, str)
+ else tuple(crossinfofile))
+
+ return fileslist
+
+def missing_files(zfile: ZipFile) -> tuple[str]:
+ """
+ Retrieve a list of files listed in the control file that do not exist in the
+ bundle.
+ """
+ def __missing_p__(thefile):
+ try:
+ zfile.getinfo(thefile)
+ return False
+ except KeyError:
+ return True
+
+ return tuple(filter(__missing_p__,
+ bundle_files_list(zfile, rqtl2.control_data(zfile))))