def _collapse_region_docs(cls, docs):
''' If the document is a hit then find parent region; pad all regions for build_info.'''
hits = [doc for doc in docs if doc.type() == 'hits']
regions = [doc for doc in docs if doc.type() == 'region']
if len(hits) > 0:
regions = Region.hits_to_regions(hits)
return regions
def _collapse_region_docs(docs):
''' If the document is a hit then find parent region; pad all regions for build_info.'''
hits = [doc for doc in docs if doc.type() == 'hits']
regions = [doc for doc in docs if doc.type() == 'region']
if len(hits) > 0:
regions = Region.hits_to_regions(hits)
for doc in hits:
docs.remove(doc)
regions = [Region.pad_region_doc(doc) for doc in regions]
for doc in regions:
if doc in docs:
docs.remove(doc)
docs.append(doc)
return len(docs)
def get_overlapping_features(self, build, seqid, start, end):
features = []
study_hits = self.get_overlapping_hits(build, seqid, start, end)
if len(study_hits) == 0:
return features
regions = Region.hits_to_regions(study_hits)
for doc in regions:
doc = Region.pad_region_doc(doc)
loc = doc.get_position(build=build).split(':')
pos = loc[1].replace(',', '').split('-')
feature = {
'name': doc.get_name(),
'id': doc.doc_id(),
'chr': loc[0],
'start': int(pos[0]),
'end': int(pos[1]) if len(pos) > 1 else int(pos[0]),
'strand': doc.get_strand_as_int(),
'attributes': {}
}
loci = doc.get_disease_loci()
sub_features = []
for locus in loci:
attributes = {}
loc = locus.get_position(build=build).split(':')
pos = loc[1].replace(',', '').split('-')
sub_feature = {
'name': locus.get_name(),
'id': locus.doc_id(),
'chr': loc[0],
'start': int(pos[0]),
'end': int(pos[1]) if len(pos) > 1 else int(pos[0]),
'strand': locus.get_strand_as_int()
}
if hasattr(locus, "disease") and getattr(locus, "disease") is not None:
attributes['disease'] = getattr(locus, "disease")
sub_feature['attributes'] = attributes
sub_features.append(sub_feature)
feature['sub_features'] = sub_features
features.append(ElasticObject(feature))
return features
def _collapse_region_docs(docs):
''' If the document is a hit then find parent region; pad all regions for build_info.'''
hits = [doc for doc in docs if doc.type() == 'hits']
regions = [doc for doc in docs if doc.type() == 'region']
if len(hits) > 0:
regions = Region.hits_to_regions(hits)
for doc in hits:
disease_locus = getattr(doc, "disease_locus")
for region in regions:
disease_loci = getattr(region, "disease_loci")
if disease_locus in disease_loci:
region.__dict__['_meta']['highlight'] = doc.highlight()
docs.remove(doc)
regions = [Region.pad_region_doc(doc) for doc in regions]
for doc in regions:
if doc in docs:
docs.remove(doc)
docs.append(doc)
return len(docs)
