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cleanup
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pori_python/ipr/annotate.py

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Original file line numberDiff line numberDiff line change
@@ -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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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")
188-
# "kbVariantId": matched_stmt["kbVariantId"],
189-
# "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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)
272-
# "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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