From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 20 Feb 2019 12:15:06 +0000 (+0000)
Subject: JAL-3187 read peptide variant from CSQ:HGVSp if present (VCF/VEP data)
X-Git-Tag: Release_2_11_1_0~59
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3425cc9c6d08acd5f82b596d51e6577b2941d9b4;p=jalview.git

JAL-3187 read peptide variant from CSQ:HGVSp if present (VCF/VEP data)
---

diff --git a/src/jalview/datamodel/MappedFeatures.java b/src/jalview/datamodel/MappedFeatures.java
index 07d3857..b69a103 100644
--- a/src/jalview/datamodel/MappedFeatures.java
+++ b/src/jalview/datamodel/MappedFeatures.java
@@ -86,10 +86,30 @@ public class MappedFeatures
     baseCodon[1] = fromSeq.getCharAt(codonPos[1] - cdsStart);
     baseCodon[2] = fromSeq.getCharAt(codonPos[2] - cdsStart);
 
-    // todo avoid duplication of code in AlignmentUtils.buildDnaVariantsMap
-
     for (SequenceFeature sf : features)
     {
+      /*
+       * VCF data may already contain the protein consequence
+       */
+      String hgvsp = sf.getValueAsString("CSQ", "HGVSp");
+      if (hgvsp != null)
+      {
+        int colonPos = hgvsp.indexOf(':');
+        if (colonPos >= 0)
+        {
+          String var = hgvsp.substring(colonPos + 1);
+          if (!vars.contains(var))
+          {
+            vars.add(var);
+          }
+          continue;
+        }
+      }
+
+      /*
+       * otherwise, compute codon and peptide variant
+       */
+      // todo avoid duplication of code in AlignmentUtils.buildDnaVariantsMap
       int cdsPos = sf.getBegin();
       if (cdsPos != sf.getEnd())
       {
@@ -138,7 +158,8 @@ public class MappedFeatures
         String peptide = ResidueProperties.codonTranslate(codon);
         if (fromResidue != peptide.charAt(0))
         {
-          String to3 = StringUtils.toSentenceCase(
+          String to3 = ResidueProperties.STOP.equals(peptide) ? "STOP"
+                  : StringUtils.toSentenceCase(
                   ResidueProperties.aa2Triplet.get(peptide));
           String var = "p." + from3 + fromPosition + to3;
           if (!vars.contains(var))