lib: several fixes in variant annotation and HGVS

opencb · Jun 4, 2021 · 28364b2 · 28364b2
1 parent 3fb0e30
commit 28364b2
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Showing 3 changed files with 7 additions and 6 deletions.
diff --git a/...b/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeCalculator.java b/...b/src/main/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeCalculator.java
@@ -168,7 +168,7 @@ protected void solveNegativeTranscript(List<ConsequenceType> consequenceTypeList
     protected char[] getReverseComplementaryCodon(String transcriptSequence, int modifiedCodonStart) {
         char[] reverseCodon = (new StringBuilder(transcriptSequence.substring(transcriptSequence.length() - modifiedCodonStart - 2,
                 // Rigth limit of the substring sums +1 because substring does not include that position
-                transcriptSequence.length() - modifiedCodonStart + 1)).reverse().toString()).toCharArray();
+                transcriptSequence.length() - modifiedCodonStart + 1)).reverse().toString().toUpperCase()).toCharArray();
         reverseCodon[0] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(reverseCodon[0]);
         reverseCodon[1] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(reverseCodon[1]);
         reverseCodon[2] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(reverseCodon[2]);
@@ -341,7 +341,7 @@ protected int updateNegativeInsertionCodonArrays(String reverseTranscriptSequenc
                                 .getResults().get(0).getSequence().charAt(0));
             } else {
                 modifiedCodonArray[modifiedCodonPosition] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(
-                        reverseTranscriptSequence.charAt(reverseTranscriptSequencePosition));
+                        reverseTranscriptSequence.toUpperCase().charAt(reverseTranscriptSequencePosition));
             }
             reverseTranscriptSequencePosition++;
 

diff --git a/...in/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeDeletionCalculator.java b/...in/java/org/opencb/cellbase/lib/variant/annotation/ConsequenceTypeDeletionCalculator.java
@@ -409,12 +409,12 @@ protected void solveStopCodonNegativeVariant(String transcriptSequence, int cdna
                                     : 0,  // Be careful reaching the end of the transcript sequence
                             // Rigth limit of the substring -2 because substring does not include that position
                             transcriptSequence.length() - cdnaVariantEnd)).reverse().toString();
-            char[] referenceCodon1Array = reverseCodon1.toCharArray();
+            char[] referenceCodon1Array = reverseCodon1.toUpperCase().toCharArray();
             referenceCodon1Array[0] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(referenceCodon1Array[0]);
             referenceCodon1Array[1] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(referenceCodon1Array[1]);
             referenceCodon1Array[2] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(referenceCodon1Array[2]);
             String referenceCodon1 = String.valueOf(referenceCodon1Array);
-            char[] referenceCodon2Array = reverseCodon2.toCharArray();
+            char[] referenceCodon2Array = reverseCodon2.toUpperCase().toCharArray();
             referenceCodon2Array[0] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(referenceCodon2Array[0]);
             referenceCodon2Array[1] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(referenceCodon2Array[1]);
             referenceCodon2Array[2] = VariantAnnotationUtils.COMPLEMENTARY_NT.get(referenceCodon2Array[2]);

diff --git a/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/hgvs/HgvsProteinCalculator.java b/cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/hgvs/HgvsProteinCalculator.java
@@ -54,7 +54,7 @@ public class HgvsProteinCalculator {
     private static final String UNIPROT_LABEL = "uniprotkb/swissprot";
     protected BuildingComponents buildingComponents = null;
 
-    public static final int MAX_NUMBER_AMINOACIDS_DISPLAYED = 10;
+    public static final int MAX_NUMBER_AMINOACIDS_DISPLAYED = 20;
 
     /**
      * Constructor.
@@ -422,7 +422,8 @@ private HgvsProtein hgvsInsertionFormatter(int aminoacidPosition, String alterna
             // Example: check 11:6390701:-:CTGGCGCTGGCG
             if (aminoacidPosition - 1 < transcript.getProteinSequence().length()) {
                 String aaAfterInsertion = transcript.getProteinSequence().substring(aminoacidPosition - 1, aminoacidPosition);
-                while (codedAminoacids.get(0).equals(aaAfterInsertion)) {
+                while (codedAminoacids.get(0).equals(aaAfterInsertion)
+                        && aminoacidPosition + 1 < transcript.getProteinSequence().length()) {
                     aminoacidPosition++;
                     aminoacids.remove(0);
                     codedAminoacids.remove(0);