draft change for test

Author: elewis2

pori_python/ipr/annotate.py

@@ -122,15 +122,22 @@ def annotate_expression_variants(
             continue
         try:
             matches = gkb_match.match_expression_variant(graphkb_conn, gene, variant)
-            for ipr_row in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
-                ipr_row["variant"] = row["key"]
-                ipr_row["variantType"] = row.get("variantType", "exp")
+            for matched_stmt in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
+                ipr_row = {
+                    'variant': row['key'],
+                    'variantType': row.get('variantType', 'exp'),
+                    'kbVariant': matched_stmt['kbVariant'],
+                    'kbMatchedStatements': [matched_stmt]
+                }
+                #ipr_row["variant"] = row["key"]
+                #ipr_row["variantType"] = row.get("variantType", "exp")
                 alterations.append(ipr_row)
         except FeatureNotFoundError as err:
             problem_genes.add(gene)
             logger.debug(f"Unrecognized gene ({gene} {variant}): {err}")
         except ValueError as err:
             logger.error(f"failed to match variants ({gene} {variant}): {err}")
+    import pdb; pdb.set_trace()
 
     if skipped:
         logger.info(f"skipped matching {skipped} expression information rows")
@@ -140,6 +147,7 @@ def annotate_expression_variants(
     logger.info(
         f"matched {len(variants)} expression variants to {len(alterations)} graphkb annotations"
     )
+    import pdb; pdb.set_trace()
     return alterations
 
 
@@ -175,10 +183,20 @@ def annotate_copy_variants(
             continue
         try:
             matches = gkb_match.match_copy_variant(graphkb_conn, gene, variant)
-            for ipr_row in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
-                ipr_row["variant"] = row["key"]
-                ipr_row["variantType"] = row.get("variantType", "cnv")
+            #for ipr_row in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
+            #    ipr_row["variant"] = row["key"]
+            #    ipr_row["variantType"] = row.get("variantType", "cnv")
+            #    alterations.append(ipr_row)
+            for matched_stmt in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
+                ipr_row = {
+                    'variant': row['key'],
+                    'variantType': row.get('variantType', 'cnv'),
+                    'kbVariant': matched_stmt['kbVariant'],
+                    'kbMatchedStatements': [matched_stmt]
+                }
                 alterations.append(ipr_row)
+                #ipr_row["variant"] = row["key"]
+                #ipr_row["variantType"] = row.get("variantType", "exp")
         except FeatureNotFoundError as err:
             problem_genes.add(gene)
             logger.debug(f"Unrecognized gene ({gene} {variant}): {err}")
@@ -252,15 +270,22 @@ def annotate_positional_variants(
                         matches = gkb_match.match_positional_variant(graphkb_conn, variant)
                     else:
                         raise parse_err
-
-                for ipr_row in get_ipr_statements_from_variants(
-                    graphkb_conn, matches, disease_name
-                ):
-                    ipr_row["variant"] = row["key"]
-                    ipr_row["variantType"] = row.get(
-                        "variantType", "mut" if row.get("gene") else "sv"
-                    )
+                for matched_stmt in get_ipr_statements_from_variants(graphkb_conn, matches, disease_name):
+                    ipr_row = {
+                        'variant': row['key'],
+                        'variantType': row.get("variantType", "mut" if row.get("gene") else "sv"),
+                        'kbVariant': matched_stmt['kbVariant'],
+                        'kbMatchedStatements': [matched_stmt]
+                    }
                     alterations.append(Hashabledict(ipr_row))
+                #for ipr_row in get_ipr_statements_from_variants(
+                #    graphkb_conn, matches, disease_name
+                #):
+                #    ipr_row["variant"] = row["key"]
+                #    ipr_row["variantType"] = row.get(
+                #        "variantType", "mut" if row.get("gene") else "sv"
+                #    )
+                #    alterations.append(Hashabledict(ipr_row))
 
             except FeatureNotFoundError as err:
                 logger.debug(f"failed to match positional variants ({variant}): {err}")
@@ -327,10 +352,18 @@ def annotate_msi(
     )
     if msi_categories:
         msi_variants = [cast(Variant, var) for var in msi_categories]
-        for ipr_row in get_ipr_statements_from_variants(graphkb_conn, msi_variants, disease_name):
-            ipr_row["variant"] = msi_category
-            ipr_row["variantType"] = "msi"
+        for matched_stmt in get_ipr_statements_from_variants(graphkb_conn, msi_variants, disease_name):
+            ipr_row = {
+                'variant': msi_category,
+                'variantType': 'msi',
+                'kbVariant': matched_stmt['kbVariant'],
+                'kbMatchedStatements': [matched_stmt]
+            }
             gkb_matches.append(ipr_row)
+        #for ipr_row in get_ipr_statements_from_variants(graphkb_conn, msi_variants, disease_name):
+        #    ipr_row["variant"] = msi_category
+        #    ipr_row["variantType"] = "msi"
+        #    gkb_matches.append(ipr_row)
     return gkb_matches
 
 
@@ -366,8 +399,16 @@ def annotate_tmb(
     )
     if categories:
         cat_variants = [cast(Variant, var) for var in categories]
-        for ipr_row in get_ipr_statements_from_variants(graphkb_conn, cat_variants, disease_name):
-            ipr_row["variant"] = category
-            ipr_row["variantType"] = "tmb"
+        for matched_stmt in get_ipr_statements_from_variants(graphkb_conn, cat_variants, disease_name):
+            ipr_row = {
+                'variant': category,
+                'variantType': 'tmb',
+                'kbVariant': matched_stmt['kbVariant'],
+                'kbMatchedStatements': [matched_stmt]
+            }
             gkb_matches.append(ipr_row)
+        #for ipr_row in get_ipr_statements_from_variants(graphkb_conn, cat_variants, disease_name):
+        #    ipr_row["variant"] = category
+        #    ipr_row["variantType"] = "tmb"
+        #    gkb_matches.append(ipr_row)
     return gkb_matches