1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.ext.htsjdk

File VCFReaderTest.java

 

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VCFReaderTest 37 77 5
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Contributing tests

This file is covered by 2 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
7    * Jalview is free software: you can redistribute it and/or
8    * modify it under the terms of the GNU General Public License
9    * as published by the Free Software Foundation, either version 3
10    * of the License, or (at your option) any later version.
11    *
12    * Jalview is distributed in the hope that it will be useful, but
13    * WITHOUT ANY WARRANTY; without even the implied warranty
14    * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15    * PURPOSE. See the GNU General Public License for more details.
16    *
17    * You should have received a copy of the GNU General Public License
18    * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19    * The Jalview Authors are detailed in the 'AUTHORS' file.
20    */
21    package jalview.ext.htsjdk;
22   
23    import static org.testng.Assert.assertEquals;
24    import static org.testng.Assert.assertFalse;
25    import static org.testng.Assert.assertTrue;
26    import htsjdk.samtools.util.CloseableIterator;
27    import htsjdk.variant.variantcontext.Allele;
28    import htsjdk.variant.variantcontext.VariantContext;
29   
30    import java.io.File;
31    import java.io.IOException;
32    import java.io.PrintWriter;
33    import java.util.List;
34   
35    import org.testng.annotations.Test;
36   
 
37    public class VCFReaderTest
38    {
39    private static final String[] VCF = new String[] { "##fileformat=VCFv4.2",
40    "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO",
41    "20\t3\t.\tC\tG\t.\tPASS\tDP=100", // SNP C/G
42    "20\t7\t.\tG\tGA\t.\tPASS\tDP=100", // insertion G/GA
43    "18\t2\t.\tACG\tA\t.\tPASS\tDP=100" }; // deletion ACG/A
44   
45    // gnomAD exome variant dataset
46    private static final String VCF_PATH = "/Volumes/gjb/smacgowan/NOBACK/resources/gnomad/gnomad.exomes.r2.0.1.sites.vcf.gz";
47   
48    // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
49   
50    /**
51    * A test to exercise some basic functionality of the htsjdk VCF reader,
52    * reading from a non-index VCF file
53    *
54    * @throws IOException
55    */
 
56  1 toggle @Test(groups = "Functional")
57    public void testReadVcf_plain() throws IOException
58    {
59  1 File f = writeVcfFile();
60  1 VCFReader reader = new VCFReader(f.getAbsolutePath());
61  1 CloseableIterator<VariantContext> variants = reader.iterator();
62   
63    /*
64    * SNP C/G variant
65    */
66  1 VariantContext vc = variants.next();
67  1 assertTrue(vc.isSNP());
68  1 Allele ref = vc.getReference();
69  1 assertEquals(ref.getBaseString(), "C");
70  1 List<Allele> alleles = vc.getAlleles();
71  1 assertEquals(alleles.size(), 2);
72  1 assertTrue(alleles.get(0).isReference());
73  1 assertEquals(alleles.get(0).getBaseString(), "C");
74  1 assertFalse(alleles.get(1).isReference());
75  1 assertEquals(alleles.get(1).getBaseString(), "G");
76   
77    /*
78    * Insertion G -> GA
79    */
80  1 vc = variants.next();
81  1 assertFalse(vc.isSNP());
82  1 assertTrue(vc.isSimpleInsertion());
83  1 ref = vc.getReference();
84  1 assertEquals(ref.getBaseString(), "G");
85  1 alleles = vc.getAlleles();
86  1 assertEquals(alleles.size(), 2);
87  1 assertTrue(alleles.get(0).isReference());
88  1 assertEquals(alleles.get(0).getBaseString(), "G");
89  1 assertFalse(alleles.get(1).isReference());
90  1 assertEquals(alleles.get(1).getBaseString(), "GA");
91   
92    /*
93    * Deletion ACG -> A
94    */
95  1 vc = variants.next();
96  1 assertFalse(vc.isSNP());
97  1 assertTrue(vc.isSimpleDeletion());
98  1 ref = vc.getReference();
99  1 assertEquals(ref.getBaseString(), "ACG");
100  1 alleles = vc.getAlleles();
101  1 assertEquals(alleles.size(), 2);
102  1 assertTrue(alleles.get(0).isReference());
103  1 assertEquals(alleles.get(0).getBaseString(), "ACG");
104  1 assertFalse(alleles.get(1).isReference());
105  1 assertEquals(alleles.get(1).getBaseString(), "A");
106   
107  1 assertFalse(variants.hasNext());
108   
109  1 variants.close();
110  1 reader.close();
111    }
112   
113    /**
114    * Creates a temporary file to be read by the htsjdk VCF reader
115    *
116    * @return
117    * @throws IOException
118    */
 
119  2 toggle protected File writeVcfFile() throws IOException
120    {
121  2 File f = File.createTempFile("Test", "vcf");
122  2 f.deleteOnExit();
123  2 PrintWriter pw = new PrintWriter(f);
124  2 for (String vcfLine : VCF)
125    {
126  10 pw.println(vcfLine);
127    }
128  2 pw.close();
129  2 return f;
130    }
131   
132    /**
133    * A 'test' that demonstrates querying an indexed VCF file for features in a
134    * specified interval
135    *
136    * @throws IOException
137    */
 
138  0 toggle @Test
139    public void testQuery_indexed() throws IOException
140    {
141    /*
142    * if not specified, assumes index file is filename.tbi
143    */
144  0 VCFReader reader = new VCFReader(VCF_PATH);
145   
146    /*
147    * gene NMT1 (human) is on chromosome 17
148    * GCHR38 (Ensembl): 45051610-45109016
149    * GCHR37 (gnoMAD): 43128978-43186384
150    * CDS begins at offset 9720, first CDS variant at offset 9724
151    */
152  0 CloseableIterator<VariantContext> features = reader.query("17",
153    43128978 + 9724, 43128978 + 9734); // first 11 CDS positions
154   
155  0 assertEquals(printNext(features), 43138702);
156  0 assertEquals(printNext(features), 43138704);
157  0 assertEquals(printNext(features), 43138707);
158  0 assertEquals(printNext(features), 43138708);
159  0 assertEquals(printNext(features), 43138710);
160  0 assertEquals(printNext(features), 43138711);
161  0 assertFalse(features.hasNext());
162   
163  0 features.close();
164  0 reader.close();
165    }
166   
167    /**
168    * Prints the toString value of the next variant, and returns its start
169    * location
170    *
171    * @param features
172    * @return
173    */
 
174  0 toggle protected int printNext(CloseableIterator<VariantContext> features)
175    {
176  0 VariantContext next = features.next();
177  0 System.out.println(next.toString());
178  0 return next.getStart();
179    }
180   
181    // "https://storage.cloud.google.com/gnomad-public/release/2.0.1/vcf/exomes/gnomad.exomes.r2.0.1.sites.vcf.gz";
182   
183    /**
184    * Test the query method that wraps a non-indexed VCF file
185    *
186    * @throws IOException
187    */
 
188  1 toggle @Test(groups = "Functional")
189    public void testQuery_plain() throws IOException
190    {
191  1 File f = writeVcfFile();
192  1 VCFReader reader = new VCFReader(f.getAbsolutePath());
193   
194    /*
195    * query for overlap of 5-8 - should find variant at 7
196    */
197  1 CloseableIterator<VariantContext> variants = reader.query("20", 5, 8);
198   
199    /*
200    * INDEL G/GA variant
201    */
202  1 VariantContext vc = variants.next();
203  1 assertTrue(vc.isIndel());
204  1 assertEquals(vc.getStart(), 7);
205  1 assertEquals(vc.getEnd(), 7);
206  1 Allele ref = vc.getReference();
207  1 assertEquals(ref.getBaseString(), "G");
208  1 List<Allele> alleles = vc.getAlleles();
209  1 assertEquals(alleles.size(), 2);
210  1 assertTrue(alleles.get(0).isReference());
211  1 assertEquals(alleles.get(0).getBaseString(), "G");
212  1 assertFalse(alleles.get(1).isReference());
213  1 assertEquals(alleles.get(1).getBaseString(), "GA");
214   
215  1 assertFalse(variants.hasNext());
216   
217  1 variants.close();
218  1 reader.close();
219    }
220    }