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Fix issue in counts #440

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Jul 25, 2024
Merged

Fix issue in counts #440

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11 changes: 10 additions & 1 deletion cmat/output_generation/clinvar_to_evidence_strings.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,7 @@ def clinvar_to_evidence_strings(string_to_efo_mappings, variant_to_gene_mappings
# Failure mode 5 (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):
if not contains_mapping(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
Expand Down Expand Up @@ -159,6 +159,10 @@ def clinvar_to_evidence_strings(string_to_efo_mappings, variant_to_gene_mappings

if evidence_strings_generated == 0:
report.clinvar_skip_invalid_evidence_string += 1
# If this record also did not have any EFO-mapped traits, it has already been counted as "skip".
# Correct this so the counts match up but we retain the more important skip reason.
if not contains_mapping(grouped_diseases):
report.clinvar_skip_missing_efo_mapping -= 1

report.complete_evidence_string_count += complete_evidence_strings_generated
report.evidence_string_count += evidence_strings_generated
Expand Down Expand Up @@ -408,3 +412,8 @@ def group_diseases_by_efo_mapping(clinvar_record_traits, string_to_efo_mappings)
selected_trait = traits[0]
grouped_tuples.append((selected_trait.preferred_or_other_valid_name, selected_trait.medgen_id, efo_id))
return grouped_tuples


def contains_mapping(grouped_diseases):
"""Checks whether any disease tuple (as described above) contains an EFO mapping."""
return any(group[-1] for group in grouped_diseases)
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