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Improve variant merging procedure, and disable merging mutations
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originating from multiple SNVs (teporarily, until sanity checks
are introduced)
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krassowski committed May 28, 2019
1 parent d278659 commit 5e66d39
Showing 1 changed file with 7 additions and 4 deletions.
11 changes: 7 additions & 4 deletions website/imports/mutations/clinvar.py
Original file line number Diff line number Diff line change
Expand Up @@ -329,10 +329,9 @@ def clinvar_parser(line):
if same_mutation_pointers:
pointer = same_mutation_pointers[0]
old = self.data_as_dict(clinvar_mutations[pointer])
new = self.data_as_dict(values, mutation_id=mutation_id)
new = self.data_as_dict(clinvar_mutation_values, mutation_id=mutation_id)

new_rs = [int(rs) for rs in (new['db_snp_ids'] or '').split('|') if rs]
for rs in new_rs:
for rs in new['db_snp_ids']:
if rs not in old['db_snp_ids']:
clinvar_mutations[pointer][1].append(rs)

Expand All @@ -343,9 +342,13 @@ def clinvar_parser(line):
index = self.insert_keys.index(key)
clinvar_mutations[pointer][index] = True

if old['variation_id'] != new['variation_id']:
print(f'Merge failed: different ids: {old["variation_id"]} != {new["variation_id"]}')
continue

print(
f'Merged details referring to the same mutation ({mutation_id}):'
f'{values} into {clinvar_mutations[pointer]}'
f'{new} into {old}'
)
continue

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