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Modify counts for when evidence is invalid #419

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merged 3 commits into from
Feb 7, 2024
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Merged

Modify counts for when evidence is invalid #419

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cea3f43
modify counts for when evidence is invalid
apriltuesday Feb 7, 2024
6b7d606
fix count and report invalid evidence
apriltuesday Feb 7, 2024
be2dd91
exit if any exception thrown and after all steps complete
apriltuesday Feb 7, 2024
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25 changes: 19 additions & 6 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 @@ -42,6 +42,7 @@ def __init__(self, trait_mappings, consequence_mappings):
self.clinvar_skip_unsupported_variation = 0
self.clinvar_skip_no_functional_consequences = 0
self.clinvar_skip_missing_efo_mapping = 0
self.clinvar_skip_invalid_evidence_string = 0
self.clinvar_done_one_complete_evidence_string = 0
self.clinvar_done_multiple_complete_evidence_strings = 0

Expand All @@ -57,17 +58,15 @@ def __init__(self, trait_mappings, consequence_mappings):
self.repeat_expansion_variants = 0
self.structural_variants = 0

def collate_report(self):
def print_report_and_check_counts(self):
# ClinVar tallies.
clinvar_fatal = self.clinvar_fatal_no_valid_traits
clinvar_skipped = (self.clinvar_skip_unsupported_variation + self.clinvar_skip_no_functional_consequences +
self.clinvar_skip_missing_efo_mapping)
self.clinvar_skip_missing_efo_mapping + self.clinvar_skip_invalid_evidence_string)
clinvar_done = (self.clinvar_done_one_complete_evidence_string +
self.clinvar_done_multiple_complete_evidence_strings)
assert clinvar_fatal + clinvar_skipped + clinvar_done == self.clinvar_total, \
'ClinVar evidence string tallies do not add up to the total amount.'

return f'''Total number of evidence strings generated\t{self.evidence_string_count}
report = f'''Total number of evidence strings generated\t{self.evidence_string_count}
Total number of complete evidence strings generated\t{self.complete_evidence_string_count}

Total number of ClinVar records\t{self.clinvar_total}
Expand All @@ -76,6 +75,7 @@ def collate_report(self):
Unsupported variation type\t{self.clinvar_skip_unsupported_variation}
No functional consequences\t{self.clinvar_skip_no_functional_consequences}
Missing EFO mapping\t{self.clinvar_skip_missing_efo_mapping}
Invalid evidence string\t{self.clinvar_skip_invalid_evidence_string}
Done: Generated at least one complete evidence string\t{clinvar_done}
One complete evidence string\t{self.clinvar_done_one_complete_evidence_string}
Multiple complete evidence strings\t{self.clinvar_done_multiple_complete_evidence_strings}
Expand All @@ -91,6 +91,14 @@ def collate_report(self):
Total number of variant to consequence mappings\t{self.total_consequence_mappings}
Number of repeat expansion variants\t{self.repeat_expansion_variants}
Number of structural variants \t{self.structural_variants}'''.replace('\n' + ' ' * 12, '\n')
print(report)

# Confirm counts as expected, exit with error if not.
expected_total = clinvar_fatal + clinvar_skipped + clinvar_done
if expected_total != self.clinvar_total:
logger.error(f'ClinVar evidence string tallies do not add up to the total amount: '
f'fatal + skipped + done = {expected_total}, total = {self.clinvar_total}')
sys.exit(1)
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def write_unmapped_terms(self, dir_out):
with open(os.path.join(dir_out, UNMAPPED_TRAITS_FILE_NAME), 'w') as unmapped_traits_file:
Expand Down Expand Up @@ -120,7 +128,7 @@ def launch_pipeline(clinvar_xml_file, efo_mapping_file, gene_mapping_file, ot_sc
report = clinvar_to_evidence_strings(
string_to_efo_mappings, variant_to_gene_mappings, clinvar_xml_file, ot_schema_file,
output_evidence_strings=os.path.join(dir_out, EVIDENCE_STRINGS_FILE_NAME))
print(report.collate_report())
report.print_report_and_check_counts()
report.write_unmapped_terms(dir_out)


Expand Down Expand Up @@ -202,10 +210,15 @@ def clinvar_to_evidence_strings(string_to_efo_mappings, variant_to_gene_mappings
elif complete_evidence_strings_generated > 1:
report.clinvar_done_multiple_complete_evidence_strings += 1

if evidence_strings_generated == 0:
report.clinvar_skip_invalid_evidence_string += 1

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

except Exception as e:
# Note while we catch exceptions here, this may or may not cause inconsistencies in the counts,
# in which case the pipeline will crash after processing all records and printing the report.
logger.error(f'Problem generating evidence for {clinvar_record.accession}')
logger.error(f'Error: {e}')
continue
Expand Down
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