Feature/ruff lint bug tests

.github/workflows/tests.yml

@@ -19,16 +19,17 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: "pip"
+          cache-dependency-path: requirements.txt
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install flake8 pytest pytest-cov coveralls
+          python -m pip install flake8 ruff pytest pytest-cov coveralls
           pip install -r requirements.txt
           pip install .
       - name: Lint with flake8
@@ -53,3 +54,5 @@ jobs:
           ./test.sh
       - name: Publish coverage to Coveralls
         uses: coverallsapp/github-action@v2.2.3
+        with:
+          parallel: true

develop.sh

@@ -0,0 +1,3 @@
+set -e
+
+pip install -e .

lint.sh

@@ -1,12 +1,5 @@
 #!/bin/bash
 set -o errexit
 
-# getting false positives due to this issue with pylint:
-# https://bitbucket.org/logilab/pylint/issues/701/false-positives-with-not-an-iterable-and
-
-find varcode tests -name '*.py' \
-  | xargs pylint \
-  --errors-only \
-  --disable=unsubscriptable-object,not-an-iterable
-
-echo 'Passes pylint check'
+ruff check varcode tests
+echo 'Passes ruff check'

tests/test_effect_helpers.py

@@ -0,0 +1,242 @@
+# 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.
+
+from varcode.effects.effect_helpers import (
+    changes_exonic_splice_site,
+    variant_overlaps_interval,
+)
+
+
+class DummyTranscript(object):
+    def __init__(self, sequence, n_exons=2):
+        self.sequence = sequence
+        self.exons = [object()] * n_exons
+
+
+def test_variant_overlaps_interval_single_base_at_interval_boundaries():
+    assert variant_overlaps_interval(
+        variant_start=3,
+        n_ref_bases=1,
+        interval_start=3,
+        interval_end=5)
+    assert variant_overlaps_interval(
+        variant_start=5,
+        n_ref_bases=1,
+        interval_start=3,
+        interval_end=5)
+
+
+def test_variant_overlaps_interval_excludes_adjacent_bases():
+    assert not variant_overlaps_interval(
+        variant_start=2,
+        n_ref_bases=1,
+        interval_start=3,
+        interval_end=5)
+    assert not variant_overlaps_interval(
+        variant_start=6,
+        n_ref_bases=1,
+        interval_start=3,
+        interval_end=5)
+
+
+def test_variant_overlaps_interval_spanning_variants():
+    assert variant_overlaps_interval(
+        variant_start=2,
+        n_ref_bases=2,
+        interval_start=3,
+        interval_end=5)
+    assert not variant_overlaps_interval(
+        variant_start=1,
+        n_ref_bases=2,
+        interval_start=3,
+        interval_end=5)
+
+
+def test_variant_overlaps_interval_insertions():
+    assert variant_overlaps_interval(
+        variant_start=3,
+        n_ref_bases=0,
+        interval_start=3,
+        interval_end=5)
+    assert variant_overlaps_interval(
+        variant_start=5,
+        n_ref_bases=0,
+        interval_start=3,
+        interval_end=5)
+    assert not variant_overlaps_interval(
+        variant_start=2,
+        n_ref_bases=0,
+        interval_start=3,
+        interval_end=5)
+
+
+def test_changes_exonic_splice_site_breaking_substitution_in_motif():
+    transcript = DummyTranscript("AATCAGAA")
+    result = changes_exonic_splice_site(
+        transcript_offset=4,
+        transcript=transcript,
+        transcript_ref="A",
+        transcript_alt="C",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is True
+
+
+def test_changes_exonic_splice_site_preserving_substitution_in_motif():
+    transcript = DummyTranscript("AATCAGAA")
+    result = changes_exonic_splice_site(
+        transcript_offset=3,
+        transcript=transcript,
+        transcript_ref="C",
+        transcript_alt="A",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is None
+
+
+def test_changes_exonic_splice_site_ignores_noncanonical_reference_motif():
+    # Exon-end motif is CTG (not MAG), so this path should not trigger.
+    transcript = DummyTranscript("AATCTGAA")
+    result = changes_exonic_splice_site(
+        transcript_offset=4,
+        transcript=transcript,
+        transcript_ref="T",
+        transcript_alt="A",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is None
+
+
+def test_changes_exonic_splice_site_skips_end_motif_check_for_last_exon():
+    # Last exon has no downstream splice donor boundary in this model.
+    transcript = DummyTranscript("AATCAGAA", n_exons=1)
+    result = changes_exonic_splice_site(
+        transcript_offset=4,
+        transcript=transcript,
+        transcript_ref="A",
+        transcript_alt="C",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is None
+
+
+def test_changes_exonic_splice_site_breaking_deletion_in_motif():
+    transcript = DummyTranscript("AATCAGAA")
+    result = changes_exonic_splice_site(
+        transcript_offset=4,
+        transcript=transcript,
+        transcript_ref="A",
+        transcript_alt="",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is True
+
+
+def test_changes_exonic_splice_site_preserving_insertion_in_motif():
+    transcript = DummyTranscript("AATCAGAA")
+    result = changes_exonic_splice_site(
+        transcript_offset=3,
+        transcript=transcript,
+        transcript_ref="",
+        transcript_alt="A",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is None
+
+
+def test_changes_exonic_splice_site_breaking_insertion_in_motif():
+    transcript = DummyTranscript("AATCAGAA")
+    result = changes_exonic_splice_site(
+        transcript_offset=3,
+        transcript=transcript,
+        transcript_ref="",
+        transcript_alt="T",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is True
+
+
+def test_changes_exonic_splice_site_breaking_acceptor_purine_substitution():
+    # Exon start base A->T for exon_number > 1 should break YAG|R.
+    transcript = DummyTranscript("CCATGGTT", n_exons=2)
+    result = changes_exonic_splice_site(
+        transcript_offset=2,
+        transcript=transcript,
+        transcript_ref="A",
+        transcript_alt="T",
+        exon_start_offset=2,
+        exon_end_offset=5,
+        exon_number=2)
+    assert result is True
+
+
+def test_changes_exonic_splice_site_preserving_acceptor_purine_substitution():
+    transcript = DummyTranscript("CCATGGTT", n_exons=2)
+    result = changes_exonic_splice_site(
+        transcript_offset=2,
+        transcript=transcript,
+        transcript_ref="A",
+        transcript_alt="G",
+        exon_start_offset=2,
+        exon_end_offset=5,
+        exon_number=2)
+    assert result is None
+
+
+def test_changes_exonic_splice_site_breaking_acceptor_deletion():
+    # Deleting the first exon base (A) reveals C (non-purine) at exon start.
+    transcript = DummyTranscript("CCACGGTT", n_exons=2)
+    result = changes_exonic_splice_site(
+        transcript_offset=2,
+        transcript=transcript,
+        transcript_ref="A",
+        transcript_alt="",
+        exon_start_offset=2,
+        exon_end_offset=5,
+        exon_number=2)
+    assert result is True
+
+
+def test_changes_exonic_splice_site_preserving_acceptor_deletion():
+    # Deleting first exon base (A) reveals G (purine), preserving YAG|R.
+    transcript = DummyTranscript("CCAGGGTT", n_exons=2)
+    result = changes_exonic_splice_site(
+        transcript_offset=2,
+        transcript=transcript,
+        transcript_ref="A",
+        transcript_alt="",
+        exon_start_offset=2,
+        exon_end_offset=5,
+        exon_number=2)
+    assert result is None
+
+
+def test_changes_exonic_splice_site_ignores_variant_before_splice_window():
+    # The canonical exon-end splice motif is at offsets 3..5: CAG.
+    # Variant is at offset 2, immediately before that window.
+    transcript = DummyTranscript("AATCAGAA")
+    result = changes_exonic_splice_site(
+        transcript_offset=2,
+        transcript=transcript,
+        transcript_ref="T",
+        transcript_alt="C",
+        exon_start_offset=0,
+        exon_end_offset=5,
+        exon_number=1)
+    assert result is None