Merge pull request #5090 from broadinstitute/codon-search

Codon search

Author: hanars

seqr/utils/search/search_utils_tests.py

@@ -284,7 +284,6 @@ def _get_expected_search_call(self, results_cache, search_fields=None, has_gene_
                                    dataset_type=None, secondary_dataset_type=None, exclude_keys=None, exclude_key_pairs=None,
                                    exclude_locations=False, exclude=None, annotations=None, annotations_secondary=None, single_gene_search=False, **kwargs):
         genes = intervals = None
-        has_included_gene_search = has_gene_search and not exclude_locations
         if has_gene_search:
             genes = {'ENSG00000186092': mock.ANY, 'ENSG00000227232': mock.ANY}
             intervals = [{'chrom': '2', 'start': 1234, 'end': 5678, 'offset': None}, {'chrom': '7', 'start': 100, 'end': 10100, 'offset': 0.1}]
@@ -296,7 +295,7 @@ def _get_expected_search_call(self, results_cache, search_fields=None, has_gene_
             'inheritance_mode': inheritance_mode,
             'inheritance_filter': {},
             'skipped_samples': mock.ANY,
-            'dataset_type': None if has_included_gene_search else dataset_type,
+            'dataset_type': dataset_type,
             'secondary_dataset_type': secondary_dataset_type,
             'exclude_locations': exclude_locations,
             'genes': genes,
@@ -490,6 +489,22 @@ def _mock_get_variants(families, search, user, previous_search_results, genome_v
             inheritance_mode='any_affected', exclude={'clinvar': ['benign']}, search_fields=['exclude'],
         )
 
+        del self.search_model.search['exclude']
+        self.search_model.search['exclude_svs'] = True
+        query_variants(self.results_model, user=self.user)
+        self._test_expected_search_call(
+            mock_get_variants, results_cache, sort='xpos', page=1, num_results=100, skip_genotype_filter=False,
+            inheritance_mode='any_affected', omitted_sample_guids=SV_SAMPLES, dataset_type='SNV_INDEL',
+        )
+
+        self.search_model.search['locus'] = {'rawItems': 'WASH7P'}
+        query_variants(self.results_model, user=self.user)
+        self._test_expected_search_call(
+            mock_get_variants, results_cache, sort='xpos', page=1, num_results=100, skip_genotype_filter=False,
+            inheritance_mode='any_affected', has_gene_search=True, single_gene_search=True,
+            omitted_sample_guids=NON_SNP_INDEL_SAMPLES, dataset_type='SNV_INDEL_only',
+        )
+
     def _test_exclude_previous_search(self, mock_get_variants, *args, num_searches=1, **kwargs):
         self._test_expected_search_call(mock_get_variants, *args, **kwargs)
         self.assertEqual(mock_get_variants.call_count, num_searches)

seqr/utils/search/utils.py

@@ -464,7 +464,7 @@ def _search_dataset_type(search, genome_version):
     chroms = [gene[f'chromGrch{genome_version}'] for gene in (search.get('genes') or {}).values()] + [
         interval['chrom'] for interval in (search.get('intervals') or [])
     ] if not search.get('exclude_locations') else None
-    dataset_type = _annotation_dataset_type(search.get('annotations'), chroms, pathogenicity=search.get('pathogenicity'))
+    dataset_type = _annotation_dataset_type(search.get('annotations'), chroms, pathogenicity=search.get('pathogenicity'), exclude_svs=search.pop('exclude_svs', False))
     secondary_dataset_type = _annotation_dataset_type(search['annotations_secondary'], chroms) if search.get('annotations_secondary') else None
 
     return dataset_type, secondary_dataset_type, None
@@ -486,15 +486,15 @@ def _chromosome_filter_dataset_type(chroms, any_sv):
     return ALL_DATA_TYPES if any_sv else Sample.DATASET_TYPE_VARIANT_CALLS
 
 
-def _annotation_dataset_type(annotations, chroms, pathogenicity=None):
+def _annotation_dataset_type(annotations, chroms, pathogenicity=None, exclude_svs=False):
     if not (annotations or chroms):
-        return Sample.DATASET_TYPE_VARIANT_CALLS if pathogenicity else None
+        return Sample.DATASET_TYPE_VARIANT_CALLS if (pathogenicity or exclude_svs) else None
 
     annotation_types = set((annotations or {}).keys())
     if annotations and annotation_types.issubset(SV_ANNOTATION_TYPES) and not pathogenicity:
         return Sample.DATASET_TYPE_SV_CALLS
 
-    no_svs = (annotations and annotation_types.isdisjoint(SV_ANNOTATION_TYPES))
+    no_svs = exclude_svs or (annotations and annotation_types.isdisjoint(SV_ANNOTATION_TYPES))
     if chroms:
         return _chromosome_filter_dataset_type(chroms, any_sv=not no_svs)
     elif no_svs:

ui/shared/components/buttons/SearchResultsLink.jsx

@@ -34,6 +34,9 @@ const mapDispatchToProps = (dispatch, ownProps) => ({
     if (ownProps.svType) {
       search.annotations = { [VEP_GROUP_SV]: [ownProps.svType, `gCNV_${ownProps.svType}`] }
     }
+    if (ownProps.excludeSvs) {
+      search.exclude_svs = ownProps.excludeSvs
+    }
     const familyGuids = ownProps.familyGuid ? [ownProps.familyGuid] : ownProps.familyGuids
     const projectFamilies = familyGuids && [{ familyGuids }]
     dispatch(navigateSavedHashedSearch(

ui/shared/components/panel/variants/Annotations.jsx

@@ -17,7 +17,7 @@ import {
 } from 'redux/selectors'
 import { HorizontalSpacer, VerticalSpacer } from '../../Spacers'
 import CopyToClipboardButton from '../../buttons/CopyToClipboardButton'
-import SearchResultsLink from '../../buttons/SearchResultsLink'
+import SearchResultsLink, { PermissiveGeneSearchLink } from '../../buttons/SearchResultsLink'
 import Modal from '../../modal/Modal'
 import { ButtonLink, HelpIcon } from '../../StyledComponents'
 import RnaSeqJunctionOutliersTable from '../../table/RnaSeqJunctionOutliersTable'
@@ -112,6 +112,9 @@ const DividedLink = styled.a.attrs({ target: '_blank', rel: 'noreferrer' })`
 
 const DividedButtonLink = DividedLink.withComponent(ButtonLink)
 
+const BaseDividedGeneSearchLink = DividedLink.withComponent(PermissiveGeneSearchLink)
+const DividedGeneSearchLink = props => <BaseDividedGeneSearchLink {...props} />
+
 const UcscBrowserLink = ({ genomeVersion, chrom, pos, refLength, endOffset, copyPosition }) => {
   const posInt = parseInt(pos, 10)
   const ucscGenomeVersion = genomeVersion === GENOME_VERSION_37 ? '19' : genomeVersion
@@ -366,13 +369,21 @@ const variantSearchLinks = (variant, mainTranscript, genesById, user, elasticsea
     </NavLink>
   )
 
+  const seqrLinks = [{
+    key: 'seqr-search',
+    trigger: seqrSearchLink,
+    content: `Search for this variant across all your seqr projects${svType ? '. Any structural variant with ≥20% reciprocal overlap will be returned.' : ''}`,
+  }]
+  if (!svType) {
+    seqrLinks.push({
+      key: 'codon-search',
+      trigger: <DividedGeneSearchLink buttonText="seqr codon" genomeVersion={genomeVersion} location={`${chrom}:${pos - 2}-${pos + 2}`} excludeSvs />,
+      content: 'Search for variants within 2bp of this variant across all your seqr projects in any affected individual and with AF < 3%',
+    })
+  }
+
   return [
-    <Popup
-      key="seqr-search"
-      trigger={seqrSearchLink}
-      content={`Search for this variant across all your seqr projects${svType ? '. Any structural variant with ≥20% reciprocal overlap will be returned.' : ''}`}
-      size="tiny"
-    />,
+    ...seqrLinks.map(props => <Popup size="tiny" {...props} />),
     ...VARIANT_LINKS.filter(({ shouldShow }) => shouldShow(linkVariant, user)).map(
       ({ name, getHref }) => <DividedLink key={name} href={getHref(linkVariant)}>{name}</DividedLink>,
     ),