@@ -128,10 +128,6 @@ def annotate_expression_variants(
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for ipr_row in get_ipr_statements_from_variants (graphkb_conn , matches , disease_name ):
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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 )
@@ -185,9 +181,6 @@ def annotate_copy_variants(
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for ipr_row in get_ipr_statements_from_variants (graphkb_conn , matches , disease_name ):
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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 )
@@ -269,9 +262,6 @@ def annotate_positional_variants(
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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 :
@@ -345,9 +335,6 @@ def annotate_msi(
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for ipr_row in get_ipr_statements_from_variants (graphkb_conn , msi_variants , disease_name ):
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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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@@ -389,8 +376,5 @@ def annotate_tmb(
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for ipr_row in get_ipr_statements_from_variants (graphkb_conn , cat_variants , disease_name ):
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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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