X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2Fvcf%2FVCFLoaderTest.java;h=246337d6e8f9dfcf784e0e401b95ad8c649267b0;hb=0a680b4ff1aaad7580d3b10941233307e2190be4;hp=4a254d29f334dd63101e2078d783db1198ff5d5c;hpb=353109c11d706b29ae5bc9606f0e12223aa45a98;p=jalview.git

diff --git a/test/jalview/io/vcf/VCFLoaderTest.java b/test/jalview/io/vcf/VCFLoaderTest.java
index 4a254d2..246337d 100644
--- a/test/jalview/io/vcf/VCFLoaderTest.java
+++ b/test/jalview/io/vcf/VCFLoaderTest.java
@@ -1,8 +1,8 @@
 package jalview.io.vcf;
 
 import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.Mapping;
@@ -21,7 +21,9 @@ import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
 import java.util.List;
+import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class VCFLoaderTest
@@ -55,7 +57,7 @@ public class VCFLoaderTest
 
   private static final String[] VCF = { "##fileformat=VCFv4.2",
       "##INFO=<ID=AF,Number=A,Type=Float,Description=\"Allele Frequency, for each ALT allele, in the same order as listed\">",
-      "##reference=GRCh38",
+      "##reference=Homo_sapiens/GRCh38",
       "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
       // A/T,C variants in position 2 of gene sequence (precedes transcript)
       // should create 2 variant features with respective scores
@@ -64,6 +66,17 @@ public class VCFLoaderTest
       // insertion G/GA is transferred to nucleotide but not to peptide
       "17\t45051613\t.\tG\tGA,C\t1666.64\tRF\tAC=15;AF=3.0e-03,2.0e-03" };
 
+  @BeforeClass
+  public void setUp()
+  {
+    /*
+     * configure to capture all available VCF and VEP (CSQ) fields
+     */
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
+    Cache.setProperty("VCF_FIELDS", ".*");
+    Cache.setProperty("VEP_FIELDS", ".*");
+  }
+
   @Test(groups = "Functional")
   public void testDoLoad() throws IOException
   {
@@ -191,7 +204,8 @@ public class VCFLoaderTest
     SequenceI gene1 = alignment.findName("gene1");
     int[] to = new int[] { 45051610, 45051634 };
     int[] from = new int[] { gene1.getStart(), gene1.getEnd() };
-    gene1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
+    gene1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+            1, 1));
 
     /*
      * map 'transcript1' to chromosome via 'gene1'
@@ -201,7 +215,8 @@ public class VCFLoaderTest
     to = new int[] { 45051612, 45051619, 45051624, 45051633 };
     SequenceI transcript1 = alignment.findName("transcript1");
     from = new int[] { transcript1.getStart(), transcript1.getEnd() };
-    transcript1.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+    transcript1.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+            from, to,
             1, 1));
 
     /*
@@ -210,7 +225,8 @@ public class VCFLoaderTest
     SequenceI gene2 = alignment.findName("gene2");
     to = new int[] { 45051634, 45051610 };
     from = new int[] { gene2.getStart(), gene2.getEnd() };
-    gene2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to, 1, 1));
+    gene2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(from, to,
+            1, 1));
 
     /*
      * map 'transcript2' to chromosome via 'gene2'
@@ -220,7 +236,8 @@ public class VCFLoaderTest
     to = new int[] { 45051633, 45051624, 45051619, 45051612 };
     SequenceI transcript2 = alignment.findName("transcript2");
     from = new int[] { transcript2.getStart(), transcript2.getEnd() };
-    transcript2.setGeneLoci("human", "GRCh38", "17", new MapList(from, to,
+    transcript2.setGeneLoci("homo_sapiens", "GRCh38", "17", new MapList(
+            from, to,
             1, 1));
 
     /*
@@ -248,7 +265,8 @@ public class VCFLoaderTest
     SequenceI gene3 = alignment.findName("gene3");
     to = new int[] { 45051610, 45051634 };
     from = new int[] { gene3.getStart(), gene3.getEnd() };
-    gene3.setGeneLoci("human", "GRCh38", "5", new MapList(from, to, 1, 1));
+    gene3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(from, to,
+            1, 1));
 
     /*
      * map 'transcript3' to chromosome
@@ -256,7 +274,8 @@ public class VCFLoaderTest
     SequenceI transcript3 = alignment.findName("transcript3");
     to = new int[] { 45051612, 45051619, 45051624, 45051633 };
     from = new int[] { transcript3.getStart(), transcript3.getEnd() };
-    transcript3.setGeneLoci("human", "GRCh38", "5", new MapList(from, to,
+    transcript3.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+            from, to,
             1, 1));
 
     /*
@@ -266,7 +285,8 @@ public class VCFLoaderTest
     to = new int[] { 45051615, 45051617, 45051619, 45051632, 45051634,
         45051634 };
     from = new int[] { transcript4.getStart(), transcript4.getEnd() };
-    transcript4.setGeneLoci("human", "GRCh38", "5", new MapList(from, to,
+    transcript4.setGeneLoci("homo_sapiens", "GRCh38", "5", new MapList(
+            from, to,
             1, 1));
 
     /*
@@ -425,49 +445,56 @@ public class VCFLoaderTest
     assertEquals(sf.getScore(), 0.1f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,A");
     // gene features include Consequence for all transcripts
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    Map map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(1);
     assertEquals(sf.getBegin(), 5);
     assertEquals(sf.getEnd(), 5);
     assertEquals(sf.getScore(), 0.2f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(2);
     assertEquals(sf.getBegin(), 9);
     assertEquals(sf.getEnd(), 11); // deletion over 3 positions
     assertEquals(sf.getScore(), 0.3f, DELTA);
     assertEquals(sf.getValue("alleles"), "CGG,C");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(3);
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
     assertEquals(sf.getScore(), 0.5f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(4);
     assertEquals(sf.getBegin(), 13);
     assertEquals(sf.getEnd(), 13);
     assertEquals(sf.getScore(), 0.4f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(5);
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17);
     assertEquals(sf.getScore(), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     sf = geneFeatures.get(6);
     assertEquals(sf.getBegin(), 17);
     assertEquals(sf.getEnd(), 17); // insertion
     assertEquals(sf.getScore(), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 2);
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
 
     /*
      * verify variant feature(s) added to transcript3
@@ -485,24 +512,25 @@ public class VCFLoaderTest
     assertEquals(sf.getScore(), 0.2f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
     // transcript features only have Consequence for that transcripts
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+    map = (Map) sf.getValue("CSQ");
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
     sf = transcriptFeatures.get(2);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript3"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript3");
 
     /*
      * verify variants computed on protein product for transcript3
@@ -541,31 +569,31 @@ public class VCFLoaderTest
     assertEquals(sf.getEnd(), 7);
     assertEquals(sf.getScore(), 0.5f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,T");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
     sf = transcriptFeatures.get(1);
     assertEquals(sf.getBegin(), 7);
     assertEquals(sf.getEnd(), 7);
     assertEquals(sf.getScore(), 0.4f, DELTA);
     assertEquals(sf.getValue("alleles"), "C,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
     sf = transcriptFeatures.get(2);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.7f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,G");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
 
     sf = transcriptFeatures.get(3);
     assertEquals(sf.getBegin(), 11);
     assertEquals(sf.getEnd(), 11);
     assertEquals(sf.getScore(), 0.6f, DELTA);
     assertEquals(sf.getValue("alleles"), "A,AC");
-    assertEquals(((String) sf.getValue("CSQ")).split(",").length, 1);
-    assertTrue(sf.getValue("CSQ").toString().contains("transcript4"));
+    assertEquals(map.size(), 9);
+    assertEquals(sf.getValueAsString("CSQ", "Feature"), "transcript4");
   }
 }