commit to save

Author: elewis2

pori_python/ipr/annotate.py

@@ -47,7 +47,9 @@ def get_second_pass_variants(
     }
 
     for reference1, variant_type in inferred_variants:
-        variants = gkb_match.match_category_variant(graphkb_conn, reference1, variant_type)
+        variants = gkb_match.match_category_variant(
+            graphkb_conn, reference1, variant_type
+        )
 
         for variant in variants:
             all_inferred_matches[variant["@rid"]] = variant
@@ -80,7 +82,8 @@ def get_ipr_statements_from_variants(
     inferred_statements = [
         s
         for s in get_statements_from_variants(graphkb_conn, inferred_matches)
-        if s["@rid"] not in existing_statements  # do not duplicate if non-inferred match
+        if s["@rid"]
+        not in existing_statements  # do not duplicate if non-inferred match
     ]
 
     for ipr_row in convert_statements_to_alterations(
@@ -125,16 +128,15 @@ def annotate_expression_variants(
             continue
         try:
             matches = gkb_match.match_expression_variant(graphkb_conn, gene, variant)
-            for matched_stmt in get_ipr_statements_from_variants(
+            for ipr_row in get_ipr_statements_from_variants(
                 graphkb_conn, matches, disease_name
             ):
-                ipr_row = {
-                    "variant": row["key"],
-                    "variantType": row.get("variantType", "exp"),
-                    "kbVariantId": matched_stmt["kbVariantId"],
-                    "kbVariant": matched_stmt["kbVariant"],
-                    "kbMatchedStatements": [matched_stmt],
-                }
+                ipr_row["variant"] = row["key"]
+                ipr_row["variantType"] = row.get("variantType", "exp")
+                # "kbVariantId": matched_stmt["kbVariantId"],
+                # "kbVariant": matched_stmt["kbVariant"],
+                # "kbMatchedStatements": [matched_stmt],
+
                 alterations.append(ipr_row)
         except FeatureNotFoundError as err:
             problem_genes.add(gene)
@@ -181,20 +183,20 @@ def annotate_copy_variants(
         if variant not in REPORTED_COPY_VARIANTS:
             # https://www.bcgsc.ca/jira/browse/GERO-77
             skipped += 1
-            logger.debug(f"Dropping {gene} copy change '{variant}' - not in REPORTED_COPY_VARIANTS")
+            logger.debug(
+                f"Dropping {gene} copy change '{variant}' - not in REPORTED_COPY_VARIANTS"
+            )
             continue
         try:
             matches = gkb_match.match_copy_variant(graphkb_conn, gene, variant)
-            for matched_stmt in get_ipr_statements_from_variants(
+            for ipr_row in get_ipr_statements_from_variants(
                 graphkb_conn, matches, disease_name
             ):
-                ipr_row = {
-                    "variant": row["key"],
-                    "variantType": row.get("variantType", "cnv"),
-                    "kbVariantId": matched_stmt["kbVariantId"],
-                    "kbVariant": matched_stmt["kbVariant"],
-                    "kbMatchedStatements": [matched_stmt],
-                }
+                ipr_row["variant"] = row["key"]
+                ipr_row["variantType"] = row.get("variantType", "cnv")
+                # "kbVariantId": matched_stmt["kbVariantId"],
+                # "kbVariant": matched_stmt["kbVariant"],
+                # "kbMatchedStatements": [matched_stmt],
                 alterations.append(ipr_row)
         except FeatureNotFoundError as err:
             problem_genes.add(gene)
@@ -208,7 +210,9 @@ def annotate_copy_variants(
         )
     if problem_genes:
         logger.error(f"gene finding failures for copy variants {sorted(problem_genes)}")
-        logger.error(f"gene finding failure for {len(problem_genes)} copy variant genes")
+        logger.error(
+            f"gene finding failure for {len(problem_genes)} copy variant genes"
+        )
     logger.info(
         f"matched {len(variants)} copy category variants to {len(alterations)} graphkb annotations"
     )
@@ -266,19 +270,21 @@ def annotate_positional_variants(
                             f"Assuming malformed deletion variant {variant} is {variant[:-2] + 'del'}"
                         )
                         variant = variant[:-2] + "del"
-                        matches = gkb_match.match_positional_variant(graphkb_conn, variant)
+                        matches = gkb_match.match_positional_variant(
+                            graphkb_conn, variant
+                        )
                     else:
                         raise parse_err
-                for matched_stmt in get_ipr_statements_from_variants(
+                for ipr_row 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"],
-                        "kbVariantId": matched_stmt["kbVariantId"],
-                        "kbMatchedStatements": [matched_stmt],
-                    }
+                    ipr_row["variant"] = row["key"]
+                    ipr_row["variantType"] = row.get(
+                        "variantType", "mut" if row.get("gene") else "sv"
+                    )
+                    # "kbVariant": matched_stmt["kbVariant"],
+                    # "kbVariantId": matched_stmt["kbVariantId"],
+                    # "kbMatchedStatements": [matched_stmt],
                     alterations.append(Hashabledict(ipr_row))
 
             except FeatureNotFoundError as err:
@@ -301,7 +307,9 @@ def annotate_positional_variants(
 
     if problem_genes:
         logger.error(f"gene finding failures for {sorted(problem_genes)}")
-        logger.error(f"{len(problem_genes)} gene finding failures for positional variants")
+        logger.error(
+            f"{len(problem_genes)} gene finding failures for positional variants"
+        )
     if errors:
         logger.error(f"skipped {errors} positional variants due to errors")
 
@@ -349,16 +357,14 @@ def annotate_msi(
     )
     if msi_categories:
         msi_variants = [cast(Variant, var) for var in msi_categories]
-        for matched_stmt in get_ipr_statements_from_variants(
+        for ipr_row in get_ipr_statements_from_variants(
             graphkb_conn, msi_variants, disease_name
         ):
-            ipr_row = {
-                "variant": msi_category,
-                "variantType": "msi",
-                "kbVariantId": matched_stmt["kbVariantId"],
-                "kbVariant": matched_stmt["kbVariant"],
-                "kbMatchedStatements": [matched_stmt],
-            }
+            ipr_row["variant"] = msi_category
+            ipr_row["variantType"] = "msi"
+            # "kbVariantId": matched_stmt["kbVariantId"],
+            # "kbVariant": matched_stmt["kbVariant"],
+            # "kbMatchedStatements": [matched_stmt],
             gkb_matches.append(ipr_row)
     return gkb_matches
 
@@ -387,7 +393,9 @@ def annotate_tmb(
                 "filters": {
                     "reference1": {
                         "target": "Signature",
-                        "filters": {"OR": [{"name": category}, {"displayName": category}]},
+                        "filters": {
+                            "OR": [{"name": category}, {"displayName": category}]
+                        },
                     }
                 },
             },
@@ -397,15 +405,13 @@ def annotate_tmb(
     )
     if categories:
         cat_variants = [cast(Variant, var) for var in categories]
-        for matched_stmt in get_ipr_statements_from_variants(
+        for ipr_row in get_ipr_statements_from_variants(
             graphkb_conn, cat_variants, disease_name
         ):
-            ipr_row = {
-                "variant": category,
-                "variantType": "tmb",
-                "kbVariantId": matched_stmt["kbVariantId"],
-                "kbVariant": matched_stmt["kbVariant"],
-                "kbMatchedStatements": [matched_stmt],
-            }
+            ipr_row["variant"] = category
+            ipr_row["variantType"] = "tmb"
+            # "kbVariantId": matched_stmt["kbVariantId"],
+            # "kbVariant": matched_stmt["kbVariant"],
+            # "kbMatchedStatements": [matched_stmt],
             gkb_matches.append(ipr_row)
     return gkb_matches