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.

5 files changed, 196 insertions, 12 deletions

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"""
diff --git a/tests/r_qtl/test_files/test_geno.zip b/tests/r_qtl/test_files/test_geno.zip
new file mode 100644
index 0000000..9cac5f9
--- /dev/null
+++ b/tests/r_qtl/test_files/test_geno.zip
diff --git a/tests/r_qtl/test_files/test_geno_transposed.zip b/tests/r_qtl/test_files/test_geno_transposed.zip
new file mode 100644
index 0000000..6ce50f8
--- /dev/null
+++ b/tests/r_qtl/test_files/test_geno_transposed.zip
diff --git a/tests/r_qtl/test_r_qtl2_geno.py b/tests/r_qtl/test_r_qtl2_geno.py
new file mode 100644
index 0000000..5ebb5a9
--- /dev/null
+++ b/tests/r_qtl/test_r_qtl2_geno.py
@@ -0,0 +1,182 @@
+"""Test the parsing of the R/qtl2 geno files."""
+from pathlib import Path
+
+import pytest
+from zipfile import ZipFile
+
+from r_qtl import r_qtl2 as rqtl2
+
+@pytest.mark.unit_test
+@pytest.mark.parametrize(
+    "relpath,expected",
+    (
+        ("tests/r_qtl/test_files/test_geno.zip",
+         ({
+             "id": "1",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "2",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "3",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": None,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "4",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "5",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           },
+          {
+             "id": "6",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           },
+          {
+             "id": "7",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "8",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "9",
+             "PVV4": None,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           },
+          {
+             "id": "10",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           })),
+        ("tests/r_qtl/test_files/test_geno_transposed.zip",
+         ({
+             "id": "1",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "2",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "3",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": None,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "4",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "5",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           },
+          {
+             "id": "6",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           },
+          {
+             "id": "7",
+             "PVV4": 1,
+             "AXR-1": 1,
+             "HH.335C-Col/PhyA": 1,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "8",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 1,
+             "EC.66C": 1
+           },
+          {
+             "id": "9",
+             "PVV4": None,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           },
+          {
+             "id": "10",
+             "PVV4": 2,
+             "AXR-1": 2,
+             "HH.335C-Col/PhyA": 2,
+             "EC.480C": 2,
+             "EC.66C": 2
+           }))))
+def test_parse_geno_files(relpath,expected):
+    """
+    GIVEN: Path to a zip file with R/qtl2 data
+    WHEN: we parse the geno file
+    THEN: ensure that the data we get is as expected
+    """
+    with ZipFile(Path(relpath).absolute(), "r") as zfile:
+        assert tuple(rqtl2.genotype_data(zfile, rqtl2.control_data(zfile))) == expected
diff --git a/tests/r_qtl/test_r_qtl2.py b/tests/r_qtl/test_r_qtl2_gmap.py
index 33ff5e5..64774c2 100644
--- a/tests/r_qtl/test_r_qtl2.py
+++ b/tests/r_qtl/test_r_qtl2_gmap.py
@@ -1,4 +1,4 @@
-"""Test the parsing of the R/qtl2 data files."""
+"""Test the parsing of the R/qtl2 gmap files."""
 from pathlib import Path
 
 import pytest