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