Add additional evidence/assertion fields to the CIViC consequence annotation

civicpy/civic.py

@@ -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 ''),
+                    str(evidence.disease),
+                    '&'.join([str(drug) for drug in evidence.drugs]),
+                    str(evidence.drug_interaction_type or ""),
+                    '&'.join(["{} (HPO ID {})".format(phenotype.hpo_class, phenotype.hpo_id) for phenotype in evidence.phenotypes]),
+                    evidence.evidence_level,
+                    str(evidence.rating),
+                    "",
+                    "",
+                    "",
+                    "",
+                    "",
                 ]))
             for assertion in self.assertions:
                 if include_status is not None and assertion.status not in include_status:
@@ -664,6 +677,19 @@ def csq(self, include_status=None):
                     "",
                     str(assertion.variant_origin),
                     assertion.status,
+                    assertion.clinical_significance,
+                    assertion.evidence_direction,
+                    str(assertion.disease),
+                    '&'.join([str(drug) for drug in assertion.drugs]),
+                    str(assertion.drug_interaction_type or ''),
+                    "",
+                    "",
+                    "",
+                    "&".join([acmg_code.code for acmg_code in assertion.acmg_codes]),
+                    str(assertion.amp_level or ''),
+                    assertion.format_nccn_guideline(),
+                    str(assertion.fda_regulatory_approval or ''),
+                    str(assertion.fda_companion_test or ''),
                 ]))
             return csq
 
@@ -798,6 +824,12 @@ def evidence(self):
     def hpo_ids(self):
         return [x.hpo_id for x in self.phenotypes if x.hpo_id]
 
+    def format_nccn_guideline(self):
+        if self.nccn_guideline is None:
+            return ""
+        else:
+            return "{} (v{})".format(self.nccn_guideline, self.nccn_guideline_version)
+
 
 class User(CivicRecord):
 
@@ -896,10 +928,22 @@ def update(self):
 class Drug(CivicAttribute):
     _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({'ncit_id'})
 
+    def __str__(self):
+        if self.ncit_id is None:
+            return self.name
+        else:
+            return "{} (NCIt ID {})".format(self.name, self.ncit_id)
+
 
 class Disease(CivicAttribute):
     _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({'display_name', 'doid', 'url'})
 
+    def __str__(self):
+        if self.doid is None:
+            return self.name
+        else:
+            return "{} (DOID {})".format(self.name, self.doid)
+
 
 class Country(CivicAttribute):
     _SIMPLE_FIELDS = CivicRecord._SIMPLE_FIELDS.union({'iso', 'name'})

civicpy/exports.py

@@ -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 ',
     ]))
 
 

setup.py

@@ -30,8 +30,9 @@
     ],
     extras_require={
         'test': [
-            'pytest',
-            'pytest-cov',
+            'pytest==4.1.0',
+            'pytest-cov==2.9.0',
+            'attrs==18.2.0',
             'python-coveralls',
             'coverage<5.0',
         ],