Merge pull request #281 from opencb/TASK-7097

TASK-7097 - Port Patch 3.3.0 -> 4.0.0 Xetabase 2.3.0 -> 3.0.0

biodata-formats/src/main/java/org/opencb/biodata/formats/variant/VariantAnnotationUtils.java

@@ -0,0 +1,82 @@
+/*
+ * Copyright 2015-2020 OpenCB
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.opencb.biodata.formats.variant;
+
+import org.opencb.biodata.models.variant.avro.AlleleOrigin;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Created by fjlopez on 22/06/15.
+ */
+public class VariantAnnotationUtils {
+
+    private static final Map<String, AlleleOrigin> ORIGIN_STRING_TO_ALLELE_ORIGIN = new HashMap<>();
+    private static final Map<Character, Character> COMPLEMENTARY_NT = new HashMap<>();
+
+    static {
+
+        ///////////////////////////////////////////////////////////////////////
+        /////   ClinVar and Cosmic allele origins to SO terms   ///////////////
+        ///////////////////////////////////////////////////////////////////////
+        ORIGIN_STRING_TO_ALLELE_ORIGIN.put("germline", AlleleOrigin.germline_variant);
+        ORIGIN_STRING_TO_ALLELE_ORIGIN.put("maternal", AlleleOrigin.maternal_variant);
+        ORIGIN_STRING_TO_ALLELE_ORIGIN.put("de novo", AlleleOrigin.de_novo_variant);
+        ORIGIN_STRING_TO_ALLELE_ORIGIN.put("paternal", AlleleOrigin.paternal_variant);
+        ORIGIN_STRING_TO_ALLELE_ORIGIN.put("somatic", AlleleOrigin.somatic_variant);
+
+        COMPLEMENTARY_NT.put('A', 'T');
+        COMPLEMENTARY_NT.put('a', 't');
+        COMPLEMENTARY_NT.put('C', 'G');
+        COMPLEMENTARY_NT.put('c', 'g');
+        COMPLEMENTARY_NT.put('G', 'C');
+        COMPLEMENTARY_NT.put('g', 'c');
+        COMPLEMENTARY_NT.put('T', 'A');
+        COMPLEMENTARY_NT.put('t', 'a');
+        COMPLEMENTARY_NT.put('N', 'N');
+        COMPLEMENTARY_NT.put('n', 'n');
+    }
+
+    public static String reverseComplement(String string) {
+        return reverseComplement(string, false);
+    }
+
+    public static String reverseComplement(String string, boolean failOnUnknownNt) {
+        StringBuilder stringBuilder = new StringBuilder(string).reverse();
+        for (int i = 0; i < stringBuilder.length(); i++) {
+            char nextNt = stringBuilder.charAt(i);
+            // Protection against weird characters, e.g. alternate:"TBS" found in ClinVar
+            if (VariantAnnotationUtils.COMPLEMENTARY_NT.containsKey(nextNt)) {
+                stringBuilder.setCharAt(i, VariantAnnotationUtils.COMPLEMENTARY_NT.get(nextNt));
+            } else {
+                if (failOnUnknownNt) {
+                    throw new IllegalArgumentException("Unknown nucleotide: '" + nextNt+ "'. "
+                            + "Unable to reverse-complement sequence '" + string + "'.");
+                } else {
+                    return null;
+                }
+            }
+        }
+        return stringBuilder.toString();
+    }
+
+    public static AlleleOrigin parseAlleleOrigin(String alleleOrigin) {
+        return ORIGIN_STRING_TO_ALLELE_ORIGIN.get(alleleOrigin);
+    }
+
+}