From c687f9460ca071c714cdc9cba62449b59b001de8 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 27 Dec 2023 12:12:33 +0300
Subject: Tests: Test parsing of non-transposed geno files.

Check that the parsing of non-transposed geno files.

Leave in failing test for transposed geno files.
---
 r_qtl/r_qtl2.py | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

(limited to 'r_qtl')

diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
index a221f26..e019d99 100644
--- a/r_qtl/r_qtl2.py
+++ b/r_qtl/r_qtl2.py
@@ -50,17 +50,19 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]:
         reader = csv.DictReader(filter(lambda line: not line.startswith("#"),
                                        io.TextIOWrapper(genofile)),
                                 delimiter=cdata.get("sep", ","))
-        for row in reader:
-            yield {
-                key: thread_op(
-                    value,
-                    # replace genotype codes
-                    lambda val: cdata["genotypes"].get(val, val),
-                    # replace N/A strings
-                    lambda val: (None if val in cdata["na.strings"] else val))
-                for key,value
-                in row.items()
-            }
+        if not cdata.get("geno_transposed", False):
+            for row in reader:
+                yield {
+                    key: thread_op(
+                        value,
+                        # replace genotype codes
+                        lambda val: cdata["genotypes"].get(val, val),
+                        # replace N/A strings
+                        lambda val: (
+                            None if val in cdata["na.strings"] else val))
+                    for key,value
+                    in row.items()
+                }
 
 def map_data(zfile: ZipFile, map_type: str, cdata: dict) -> dict:
     """Read gmap files to get the genome mapping data"""
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