add testing coverage for copy_umi_from_read_name with and without removeUmi=True; add strict=True tests for extract_umis_from_read_name()

Author: emmcauley

fgpyo/sam/tests/test_umi_methods.py

@@ -1,5 +1,7 @@
 import pytest
-from fgpyo.sam import extract_umi_from_read_name, _is_valid_umi
+from fgpyo.sam import extract_umis_from_read_name, _is_valid_umi, copy_umi_from_read_name, AlignedSegment
+from fgpyo.sam.builder import SamBuilder
+
 
 @pytest.mark.parametrize(
     "umi,validity",
@@ -30,7 +32,7 @@ def test_is_valid_umi(umi: str, validity: bool) -> None:
 )
 def test_extract_umi_from_read_name(read_name: str, umi: str) -> None:
     """Test that we can extract UMI from a read name."""
-    assert extract_umi_from_read_name(read_name) == umi
+    assert extract_umis_from_read_name(read_name) == umi
 
 
 @pytest.mark.parametrize(
@@ -47,4 +49,41 @@ def test_extract_umi_from_read_name(read_name: str, umi: str) -> None:
 def test_extract_umi_from_read_name_raises(read_name: str) -> None:
     """Test that we raise an error when the read name includes an invalid UMI."""
     with pytest.raises(ValueError):
-        extract_umi_from_read_name(read_name)
+        extract_umis_from_read_name(read_name)
+
+@pytest.mark.parametrize(
+    "read_name, extraction",
+    [
+        ("abc:def:ghi:jfk:lmn:opq:ACGT",None), #colons == 6
+        ("abc:def:ghi:jfk:lmn:opq:rst:ACGT","ACGT"), #colons == 7
+    ],
+)
+def test_strict_extract_umi_from_read_name(read_name: str, extraction: str) -> None:
+    """Test that we raise an error when strict=True and number of colons is not 7 or 8."""
+    assert extract_umis_from_read_name(read_name, strict=True) == extraction
+
+@pytest.mark.parametrize(
+    "read_name",
+    [
+        ("abc:def:ghi:jfk"),
+        ("abc:def:ghi:jfk:lmn:opq:rst:uvw:xyz"),
+        ("abc:def:ghi:jfk:lmn:opq:rst:") #Invalid UMI
+    ],
+)
+def test_strict_extract_umi_from_read_name_raises(read_name: str) -> None:
+    """Test that we raise an error when strict=True and number of colons is not 7 or 8."""
+    with pytest.raises(ValueError):
+        extract_umis_from_read_name(read_name,strict=True)
+def test_copy_umi_from_read_name() -> None:
+    builder = SamBuilder()
+    read = builder.add_single(name="read_name:GATTACA")
+    copy_umi_from_read_name(read, remove_umi=False)
+    assert read.qname == "read_name:GATTACA"
+    assert read.get_tag("RX") == "GATTACA"
+
+def test_copy_remove_umi_from_read_name() -> None:
+    builder = SamBuilder()
+    read = builder.add_single(name="read_name:GATTACA")
+    copy_umi_from_read_name(read, remove_umi=True)
+    assert read.qname == "read_name"
+    assert read.get_tag("RX") == "GATTACA"