Merge pull request #150 from griffithlab/fusions

Remove reference to secondary coordinates

civicpy/__version__.py

@@ -3,7 +3,7 @@
 __url__ = 'http://civicpy.org'
 __major__ = '3'
 __minor__ = '1'
-__patch__ = '1'
+__patch__ = '2'
 __meta_label__ = ''
 __short_version__ = "{}.{}".format(__major__, __minor__)
 __version__ = "{}.{}".format(__short_version__, __patch__)

civicpy/civic.py

@@ -606,9 +606,7 @@ def is_deletion(self):
         return (ref is not None and alt is None) or (ref is not None and alt is not None and len(ref) > len(alt))
 
     def is_valid_for_vcf(self, emit_warnings=False):
-        if self.coordinates.chromosome2 or self.coordinates.start2 or self.coordinates.stop2:
-            warning = "Variant {} has a second set of coordinates. Skipping".format(self.id)
-        elif self.coordinates.chromosome and self.coordinates.start and (self.coordinates.reference_bases or self.coordinates.variant_bases):
+        if self.coordinates.chromosome and self.coordinates.start and (self.coordinates.reference_bases or self.coordinates.variant_bases):
             if self._valid_ref_bases():
                 if self._valid_alt_bases():
                     return True
@@ -2083,11 +2081,11 @@ def _build_coordinate_table(variants):
             variant_records.append([chr, start, stop, alt, ref, hash(v)])
         else:
             continue
-        start = getattr(c, 'start2', None)
-        stop = getattr(c, 'stop2', None)
-        chr = getattr(c, 'chromosome2', None)
-        if all([start, stop, chr]):
-            variant_records.append([chr, start, stop, None, None, hash(v)])
+        #start = getattr(c, 'start2', None)
+        #stop = getattr(c, 'stop2', None)
+        #chr = getattr(c, 'chromosome2', None)
+        #if all([start, stop, chr]):
+        #    variant_records.append([chr, start, stop, None, None, hash(v)])
     df = pd.DataFrame.from_records(
         variant_records,
         columns=['chr', 'start', 'stop', 'alt', 'ref', 'v_hash']

civicpy/tests/test_civic.py

@@ -359,8 +359,8 @@ def test_bulk_any_search_variants(self):
             CoordinateQuery('7', 140453136, 140453137, 'TT')
         ]
         search_results = civic.bulk_search_variants_by_coordinates(sorted_queries, search_mode='any')
-        assert len(search_results[sorted_queries[0]]) == 19
-        assert len(search_results[sorted_queries[1]]) >= 19
+        assert len(search_results[sorted_queries[0]]) == 12
+        assert len(search_results[sorted_queries[1]]) >= 13
 
     def test_bulk_exact_search_variants(self):
         sorted_queries = [
@@ -390,8 +390,8 @@ def test_bulk_re_search_variants(self):
             CoordinateQuery('7', 140453136, 140453137)
         ]
         search_results = civic.bulk_search_variants_by_coordinates(sorted_queries, search_mode='record_encompassing')
-        assert len(search_results[sorted_queries[0]]) == 19
-        assert len(search_results[sorted_queries[1]]) == 16
+        assert len(search_results[sorted_queries[0]]) == 12
+        assert len(search_results[sorted_queries[1]]) == 9
 
     def test_build38_exact_search_variants(self, v600e):
         query = CoordinateQuery('7', 140753336, 140753336, 'T', 'A', 'GRCh38')
@@ -482,10 +482,6 @@ def test_has_ncit_id(self, v600e_assertion):
 LOGGER = logging.getLogger(__name__)
 
 def test_is_valid_for_vcf_warnings(caplog):
-    fusion_variant = civic.get_variant_by_id(287)
-    fusion_variant.is_valid_for_vcf(emit_warnings=True)
-    assert "Variant 287 has a second set of coordinates. Skipping" in caplog.text
-
     incomplete_coordinates_variant = civic.get_variant_by_id(27)
     incomplete_coordinates_variant.is_valid_for_vcf(emit_warnings=True)
     assert "Incomplete coordinates for variant 27. Skipping." in caplog.text