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Add additional evidence/assertion fields to the CIViC consequence annotation #92

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merged 6 commits into from
Jun 19, 2020
Merged

Add additional evidence/assertion fields to the CIViC consequence annotation #92

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1c1fe97
Add additional evidence/assertion fields to the CIViC consequence ann…
susannasiebert Jun 1, 2020
59f2d7d
Overwrite the Disease __str__ method to control formatting of disease…
susannasiebert Jun 19, 2020
98ba619
Overwrite the Drug __str__ method to control formatting of drug with/…
susannasiebert Jun 19, 2020
49cd95f
Fix formatting for assertions without nccn_guideline
susannasiebert Jun 19, 2020
870622e
Pin pytest and pytest-cov versions to avoid version conflicts
susannasiebert Jun 19, 2020
f07021c
Pin attrs to an older version to maintain compatibility with pytest
susannasiebert Jun 19, 2020
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26 changes: 26 additions & 0 deletions civicpy/civic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -638,6 +638,19 @@ def csq(self, include_status=None):
"{} ({})".format(evidence.source.citation_id, evidence.source.source_type),
str(evidence.variant_origin),
evidence.status,
str(evidence.clinical_significance or ''),
str(evidence.evidence_direction or ''),
"{} (DOID {})".format(evidence.disease.name, evidence.disease.doid),
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'&'.join(["{} (NCIt ID {})".format(drug.name, drug.ncit_id) for drug in evidence.drugs]),
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str(evidence.drug_interaction_type or ""),
'&'.join(["{} (HPO ID {})".format(phenotype.hpo_class, phenotype.hpo_id) for phenotype in evidence.phenotypes]),
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evidence.evidence_level,
str(evidence.rating),
"",
"",
"",
"",
"",
]))
for assertion in self.assertions:
if include_status is not None and assertion.status not in include_status:
Expand All @@ -664,6 +677,19 @@ def csq(self, include_status=None):
"",
str(assertion.variant_origin),
assertion.status,
assertion.clinical_significance,
assertion.evidence_direction,
"{} (DOID {})".format(assertion.disease.name, assertion.disease.doid),
'&'.join(["{} (NCIt ID {})".format(drug.name, drug.ncit_id) for drug in assertion.drugs]),
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str(assertion.drug_interaction_type or ''),
"",
"",
"",
"&".join([acmg_code.code for acmg_code in assertion.acmg_codes]),
str(assertion.amp_level or ''),
"{} (v{})".format(assertion.nccn_guideline, assertion.nccn_guideline_version),
str(assertion.fda_regulatory_approval or ''),
str(assertion.fda_companion_test or ''),
]))
return csq

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13 changes: 13 additions & 0 deletions civicpy/exports.py
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Original file line number Diff line number Diff line change
Expand Up @@ -78,6 +78,19 @@ class VCFWriter(DictWriter):
'CIViC Entity Source',
'CIViC Entity Variant Origin',
'CIViC Entity Status',
'CIViC Entity Clinical Signifiance',
'CIViC Entity Direction',
'CIViC Entity Disease',
'CIViC Entity Drugs',
'CIViC Entity Drug Interaction Type',
'CIViC Evidence Phenotypes',
'CIViC Evidence Level',
'CIViC Evidence Rating',
'CIViC Assertion ACMG Codes',
'CIViC Assertion AMP Category',
'CIViC Assertion NCCN Guideline',
'CIVIC Assertion Regulatory Approval',
'CIVIC Assertion FDA Companion Test ',
]))


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