From 3f879d120f7628646f383a457206b15037cc57dc Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Mon, 5 Feb 2024 15:18:44 +0300
Subject: Check that data in geno file is valid

Add a function to ensure the values in the geno files are all listed
in the control data under the "genotypes" key.
---
 r_qtl/r_qtl2.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'r_qtl/r_qtl2.py')

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."""
-- 
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