fix test failures: formatting, use of deprecated qname instead of rec.query_name

Author: emmcauley

fgpyo/sam/tests/test_umi_methods.py

@@ -1,5 +1,8 @@
 import pytest
-from fgpyo.sam import extract_umis_from_read_name, _is_valid_umi, copy_umi_from_read_name, AlignedSegment
+
+from fgpyo.sam import _is_valid_umi
+from fgpyo.sam import copy_umi_from_read_name
+from fgpyo.sam import extract_umis_from_read_name
 from fgpyo.sam.builder import SamBuilder
 
 
@@ -51,39 +54,44 @@ def test_extract_umi_from_read_name_raises(read_name: str) -> None:
     with pytest.raises(ValueError):
         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
+        ("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
+        ("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)
+        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.query_name == "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"
+    assert read.query_name == "read_name"
+    assert read.get_tag("RX") == "GATTACA"