varcode 2.0.0__tar.gz → 2.2.0__tar.gz

{varcode-2.0.0/varcode.egg-info → varcode-2.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: varcode
-Version: 2.0.0
+Version: 2.2.0
 Summary: Variant annotation in Python
 Author-email: Alex Rubinsteyn <alex.rubinsteyn@unc.edu>
 Project-URL: Homepage, https://github.com/openvax/varcode

varcode-2.2.0/tests/test_collection_variants_attr_consistency.py

@@ -0,0 +1,88 @@
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""
+Regression tests for https://github.com/openvax/varcode/issues/220
+
+VariantCollection.variants was assigned the raw input list before
+Collection.__init__ sorted / de-duplicated elements, so iterating a
+VariantCollection produced one order while `.variants` produced
+another. The same pattern existed in EffectCollection.effects.
+"""
+
+import varcode
+from varcode import Variant, VariantCollection
+from varcode.effects.effect_collection import EffectCollection
+
+
+def _unsorted_variants():
+    return [
+        Variant(contig="1", start=4, ref="A", alt="T"),
+        Variant(contig="1", start=1, ref="A", alt="T"),
+        Variant(contig="1", start=3, ref="A", alt="T"),
+        Variant(contig="1", start=2, ref="A", alt="T"),
+    ]
+
+
+def test_variant_collection_variants_matches_iteration_with_default_sort():
+    vc = VariantCollection(variants=_unsorted_variants())
+    iterated = [v.start for v in vc]
+    via_attr = [v.start for v in vc.variants]
+    assert iterated == via_attr, (
+        "vc.variants should match iteration order, got %r vs %r"
+        % (via_attr, iterated)
+    )
+
+
+def test_variant_collection_variants_matches_iteration_with_sort_key_none_distinct_false():
+    # Explicitly opt out of sorting and deduplication. Iteration and
+    # .variants should both preserve the original input order.
+    variants = _unsorted_variants()
+    vc = VariantCollection(
+        variants=variants, sort_key=None, distinct=False
+    )
+    iterated = [v.start for v in vc]
+    via_attr = [v.start for v in vc.variants]
+    assert iterated == via_attr
+    # And the order should match the input.
+    assert iterated == [4, 1, 3, 2]
+
+
+def test_variant_collection_variants_matches_iteration_with_distinct_true():
+    # When distinct=True and sort_key=None, the base Collection uses
+    # set() which loses order. Regardless of what order it ends up in,
+    # iteration and .variants should agree.
+    variants = _unsorted_variants()
+    vc = VariantCollection(
+        variants=variants, sort_key=None, distinct=True
+    )
+    iterated = [v.start for v in vc]
+    via_attr = [v.start for v in vc.variants]
+    assert iterated == via_attr
+
+
+def test_variant_collection_len_matches_variants_attr():
+    vc = VariantCollection(variants=_unsorted_variants())
+    assert len(vc) == len(vc.variants)
+
+
+def test_effect_collection_effects_matches_iteration():
+    # Same bug existed in EffectCollection.effects — produce an effect
+    # collection and verify the two access paths agree.
+    variant = Variant("17", 43082575 - 5, "CCT", "GGG", "GRCh38")
+    effects = variant.effects()
+    iterated = [e.__class__.__name__ for e in effects]
+    via_attr = [e.__class__.__name__ for e in effects.effects]
+    assert iterated == via_attr, (
+        "effects.effects should match iteration order, got %r vs %r"
+        % (via_attr, iterated)
+    )