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Continue parsing records when exceptions occur in evidence generation #418

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merged 2 commits into from
Feb 5, 2024
Merged

Continue parsing records when exceptions occur in evidence generation #418

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e2757cc
continue parsing records when exceptions occur
apriltuesday Feb 5, 2024
a9cfb56
remove unneeded assertion
apriltuesday Feb 5, 2024
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1 change: 1 addition & 0 deletions cmat/clinvar_xml_io/clinvar_record.py
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ class ClinVarRecord:
score_map = {
"no assertion provided": 0,
'no assertion criteria provided': 0,
'no classifications from unflagged records': 0,
'criteria provided, single submitter': 1,
'criteria provided, conflicting interpretations': 1,
'criteria provided, multiple submitters, no conflicts': 2,
Expand Down
134 changes: 71 additions & 63 deletions cmat/output_generation/clinvar_to_evidence_strings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -101,11 +101,12 @@ def write_unmapped_terms(self, dir_out):
def validate_evidence_string(ev_string, ot_schema_contents):
try:
jsonschema.validate(ev_string, ot_schema_contents, format_checker=jsonschema.FormatChecker())
return True
except jsonschema.exceptions.ValidationError as err:
logger.error('Error: evidence string does not validate against schema.')
logger.error(f'Error message: {err}')
logger.error(f'Complete evidence string: {json.dumps(ev_string)}')
sys.exit(1)
return False
except jsonschema.exceptions.SchemaError:
logger.error('Error: OpenTargets schema file is invalid')
sys.exit(1)
Expand Down Expand Up @@ -135,72 +136,79 @@ def clinvar_to_evidence_strings(string_to_efo_mappings, variant_to_gene_mappings
if report.clinvar_total % 1000 == 0:
logger.info(f'{report.clinvar_total} records processed')

# Failure mode 1 (fatal). A ClinVar record contains no valid traits (traits which have at least one valid,
# potentially mappable name).
if not clinvar_record.traits_with_valid_names:
report.clinvar_fatal_no_valid_traits += 1
continue
# Catch any exceptions for this record so we can continue processing.
try:
# Failure mode 1 (fatal). A ClinVar record contains no valid traits (traits which have at least one valid,
# potentially mappable name).
if not clinvar_record.traits_with_valid_names:
report.clinvar_fatal_no_valid_traits += 1
continue

# Failure mode 2 (skip). A ClinVar record contains an unsupported variation type.
if clinvar_record.measure is None:
report.clinvar_skip_unsupported_variation += 1
continue
# Failure mode 2 (skip). A ClinVar record contains an unsupported variation type.
if clinvar_record.measure is None:
report.clinvar_skip_unsupported_variation += 1
continue

# Within each ClinVar record, an evidence string is generated for all possible permutations of (1) valid allele
# origins, (2) EFO mappings, and (3) genes where the variant has effect.
grouped_allele_origins = convert_allele_origins(clinvar_record.valid_allele_origins)
consequence_types, _ = get_consequence_types(clinvar_record.measure, variant_to_gene_mappings)
grouped_diseases = group_diseases_by_efo_mapping(clinvar_record.traits_with_valid_names,
string_to_efo_mappings)
# Within each ClinVar record, an evidence string is generated for all possible permutations of (1) valid allele
# origins, (2) EFO mappings, and (3) genes where the variant has effect.
grouped_allele_origins = convert_allele_origins(clinvar_record.valid_allele_origins)
consequence_types, _ = get_consequence_types(clinvar_record.measure, variant_to_gene_mappings)
grouped_diseases = group_diseases_by_efo_mapping(clinvar_record.traits_with_valid_names,
string_to_efo_mappings)

# Failure mode 3 (skip). No functional consequences are available.
if not consequence_types:
report.clinvar_skip_no_functional_consequences += 1
continue
# Failure mode 3 (skip). No functional consequences are available.
if not consequence_types:
report.clinvar_skip_no_functional_consequences += 1
continue

# Gather consequence mapping counts for variants of interest
if clinvar_record.measure.is_repeat_expansion_variant:
report.repeat_expansion_variants += len(consequence_types)
if is_structural_variant(clinvar_record.measure):
report.structural_variants += len(consequence_types)

# Failure mode 4 (skip). A ClinVar record has at least one trait with at least one valid name, but no suitable
# EFO mappings were found in the database. This will still generate an evidence string, but is tracked as a
# failure so we can continue to measure mapping coverage.
if not any(group[-1] for group in grouped_diseases):
report.clinvar_skip_missing_efo_mapping += 1
unmapped_trait_name = clinvar_record.traits_with_valid_names[0].preferred_or_other_valid_name
report.unmapped_trait_names[unmapped_trait_name] += 1

assert grouped_allele_origins and grouped_diseases and consequence_types, \
'Some of the attribute lists are still empty even after passing all checks.'

complete_evidence_strings_generated = 0
evidence_strings_generated = 0
for allele_origins, disease_attributes, consequence_attributes in itertools.product(
grouped_allele_origins, grouped_diseases, consequence_types):
disease_name, disease_source_id, disease_mapped_efo_id = disease_attributes
evidence_string = generate_evidence_string(clinvar_record, allele_origins, disease_name, disease_source_id,
disease_mapped_efo_id, consequence_attributes)

# Validate and immediately output the evidence string (not keeping everything in memory).
validate_evidence_string(evidence_string, ot_schema_contents)
output_evidence_strings_file.write(json.dumps(evidence_string) + '\n')

# Record some evidence string and trait metrics.
evidence_strings_generated += 1
if disease_mapped_efo_id is not None:
complete_evidence_strings_generated += 1
report.used_trait_mappings.add((disease_name, disease_mapped_efo_id))

assert evidence_strings_generated != 0, 'No evidence strings generated despite all attributes passing checks.'
if complete_evidence_strings_generated == 1:
report.clinvar_done_one_complete_evidence_string += 1
elif complete_evidence_strings_generated > 1:
report.clinvar_done_multiple_complete_evidence_strings += 1

report.complete_evidence_string_count += complete_evidence_strings_generated
report.evidence_string_count += evidence_strings_generated
# Gather consequence mapping counts for variants of interest
if clinvar_record.measure.is_repeat_expansion_variant:
report.repeat_expansion_variants += len(consequence_types)
if is_structural_variant(clinvar_record.measure):
report.structural_variants += len(consequence_types)

# Failure mode 4 (skip). A ClinVar record has at least one trait with at least one valid name, but no suitable
# EFO mappings were found in the database. This will still generate an evidence string, but is tracked as a
# failure so we can continue to measure mapping coverage.
if not any(group[-1] for group in grouped_diseases):
report.clinvar_skip_missing_efo_mapping += 1
unmapped_trait_name = clinvar_record.traits_with_valid_names[0].preferred_or_other_valid_name
report.unmapped_trait_names[unmapped_trait_name] += 1

assert grouped_allele_origins and grouped_diseases and consequence_types, \
'Some of the attribute lists are still empty even after passing all checks.'

complete_evidence_strings_generated = 0
evidence_strings_generated = 0
for allele_origins, disease_attributes, consequence_attributes in itertools.product(
grouped_allele_origins, grouped_diseases, consequence_types):
disease_name, disease_source_id, disease_mapped_efo_id = disease_attributes
evidence_string = generate_evidence_string(clinvar_record, allele_origins, disease_name, disease_source_id,
disease_mapped_efo_id, consequence_attributes)

# Validate and immediately output the evidence string (not keeping everything in memory).
is_valid = validate_evidence_string(evidence_string, ot_schema_contents)
if is_valid:
output_evidence_strings_file.write(json.dumps(evidence_string) + '\n')

# Record some evidence string and trait metrics.
evidence_strings_generated += 1
if disease_mapped_efo_id is not None:
complete_evidence_strings_generated += 1
report.used_trait_mappings.add((disease_name, disease_mapped_efo_id))

if complete_evidence_strings_generated == 1:
report.clinvar_done_one_complete_evidence_string += 1
elif complete_evidence_strings_generated > 1:
report.clinvar_done_multiple_complete_evidence_strings += 1

report.complete_evidence_string_count += complete_evidence_strings_generated
report.evidence_string_count += evidence_strings_generated

except Exception as e:
logger.error(f'Problem generating evidence for {clinvar_record.accession}')
logger.error(f'Error: {e}')
continue

output_evidence_strings_file.close()
return report
Expand Down
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