From aefa19252cf0dfe1cc02b2f87a4f66dc807f4f74 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Fri, 16 Feb 2024 16:45:32 +0300
Subject: Replace genotype codes with values in control file.

---
 r_qtl/r_qtl2.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index 4f0ab2a..96776b7 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -146,7 +146,8 @@ def make_process_data_geno(cdata) -> tuple[
         Callable[[str, tuple[str, ...], tuple[str, ...]],
                  tuple[dict, ...]]]:
     """Build functions to process genotype data."""
-    def replace_genotype_codes(val):
+    def replace_genotype_codes(val):#pylint: disable=[redefined-outer-name]
+        # The rewrite will probably make this obsolete.
         return cdata["genotypes"].get(val, val)
 
     def __non_transposed__(row: dict) -> dict:
@@ -313,3 +314,7 @@ def missing_value_codes_to_none(value: str,
     If 'value' is a missing value code, return `None`, otherwise return 'value'.
     """
     return value if value not in nastrings else None
+
+def replace_genotype_codes(value: str, genocodes: dict):
+    """Convert genotype codes into values specified in control file."""
+    return genocodes.get(value, value)
-- 
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