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ALS-6330: Cleanup old genomic unit tests and test data
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@ramari16
ramari16 committed May 9, 2024
1 parent 98ff360 commit b0407fc
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Showing 8 changed files with 42 additions and 1,281 deletions.
24 changes: 12 additions & 12 deletions ...c/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/BucketIndexBySampleTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,19 +38,19 @@ public class BucketIndexBySampleTest {
private static BucketIndexBySample bucketIndexBySample;

//Some known variant specs from the input file.
private static final String spec1 = "4,9856624,CAAAAA,C";
private static final String spec2 = "4,9856624,CAAA,C";
private static final String spec3 = "4,9856624,CA,C";
private static final String spec4 = "4,9856624,C,CA";
private static final String spec5 = "4,9856624,CAAAAA,CA";
private static final String spec1 = "4,9856624,CAAAAA,C,NULL,NULL";
private static final String spec2 = "4,9856624,CAAA,C,NULL,NULL";
private static final String spec3 = "4,9856624,CA,C,NULL,NULL";
private static final String spec4 = "4,9856624,C,CA,NULL,NULL";
private static final String spec5 = "4,9856624,CAAAAA,CA,NULL,NULL";

private static final String spec6 = "14,19000060,C,G";
private static final String spec7 = "14,19000152,C,T";
private static final String spec8 = "14,19007733,C,T";
private static final String spec9 = "14,19010456,T,G";
private static final String spec10 = "14,21616875,T,C"; // patient 9 and 10 are 1/.
private static final String spec11 = "14,19001521,T,C"; //patient 9 and 10 are 0/.
private static final String spec12 = "14,19022646,A,G"; //patient 7 is ./.
private static final String spec6 = "14,19000060,C,G,NULL,NULL";
private static final String spec7 = "14,19000152,C,T,NULL,NULL";
private static final String spec8 = "14,19007733,C,T,NULL,NULL";
private static final String spec9 = "14,19010456,T,G,NULL,NULL";
private static final String spec10 = "14,21616875,T,C,NULL,NULL"; // patient 9 and 10 are 1/.
private static final String spec11 = "14,19001521,T,C,NULL,NULL"; //patient 9 and 10 are 0/.
private static final String spec12 = "14,19022646,A,G,NULL,NULL"; //patient 7 is ./.

// ## Patient 1 - NO variants
// ## Patient 2 - ALL variants
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30 changes: 14 additions & 16 deletions .../test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMetadataIndexTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,6 @@
import static org.springframework.test.util.AssertionErrors.assertEquals;
import static org.springframework.test.util.AssertionErrors.assertNotNull;

// todo: enable when variant explorer is implemented
@Disabled
public class VariantMetadataIndexTest {

//From file 1 14 19038291 rs550062154 C A
Expand All @@ -34,11 +32,11 @@ public class VariantMetadataIndexTest {
VariantBucketHolder<String[]> bucketCache = new VariantBucketHolder<String[]>();

//Some known variant specs from the input file. These have been designed for testing partially overlapping specs
private static final String spec1 = "4,9856624,CAAAAA,C"; private static final String spec1Info = "AC=401;AF=8.00719e-02;NS=2504;AN=5008;EAS_AF=3.37000e-02;EUR_AF=4.97000e-02;AFR_AF=1.64100e-01;AMR_AF=3.75000e-02;SAS_AF=7.57000e-02;DP=18352;AA=G|||;VT=SNP";
private static final String spec2 = "4,9856624,CAAA,C"; private static final String spec2Info = "AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.54000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18328;AA=T|||;VT=SNP";
private static final String spec3 = "4,9856624,CA,C"; private static final String spec3Info = "AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18519;AA=T|||;VT=SNP";
private static final String spec4 = "4,9856624,C,CA"; private static final String spec4Info = "AC=75;AF=1.49760e-02;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=2.49000e-02;AFR_AF=6.80000e-03;AMR_AF=4.30000e-03;SAS_AF=5.10000e-03;DP=18008;AA=A|||;VT=SNP";
private static final String spec5 = "4,9856624,CAAAAA,CA"; private static final String spec5Info = "AC=3033;AF=6.05631e-01;NS=2504;AN=5008;EAS_AF=5.23800e-01;EUR_AF=7.54500e-01;AFR_AF=4.28900e-01;AMR_AF=7.82400e-01;SAS_AF=6.50300e-01;DP=20851;VT=INDEL";
private static final String spec1 = "4,9856624,CAAAAA,C,TVP23A,splice_acceptor_variant"; private static final String spec1Info = "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=401;AF=8.00719e-02;NS=2504;AN=5008;EAS_AF=3.37000e-02;EUR_AF=4.97000e-02;AFR_AF=1.64100e-01;AMR_AF=3.75000e-02;SAS_AF=7.57000e-02;DP=18352;AA=G|||;VT=SNP";
private static final String spec2 = "4,9856624,CAAA,C,TVP23A,splice_acceptor_variant"; private static final String spec2Info = "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=62;AF=1.23802e-02;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.00000e-03;AFR_AF=4.54000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18328;AA=T|||;VT=SNP";
private static final String spec3 = "4,9856624,CA,C,TVP23A,splice_acceptor_variant"; private static final String spec3Info = "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=8;AF=1.59744e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=6.10000e-03;AMR_AF=0.00000e+00;SAS_AF=0.00000e+00;DP=18519;AA=T|||;VT=SNP";
private static final String spec4 = "4,9856624,C,CA,TVP23A,splice_acceptor_variant"; private static final String spec4Info = "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=75;AF=1.49760e-02;NS=2504;AN=5008;EAS_AF=3.27000e-02;EUR_AF=2.49000e-02;AFR_AF=6.80000e-03;AMR_AF=4.30000e-03;SAS_AF=5.10000e-03;DP=18008;AA=A|||;VT=SNP";
private static final String spec5 = "4,9856624,CAAAAA,CA,TVP23A,splice_acceptor_variant"; private static final String spec5Info = "Gene_with_variant=TVP23A;Variant_consequence_calculated=splice_acceptor_variant;AC=3033;AF=6.05631e-01;NS=2504;AN=5008;EAS_AF=5.23800e-01;EUR_AF=7.54500e-01;AFR_AF=4.28900e-01;AMR_AF=7.82400e-01;SAS_AF=6.50300e-01;DP=20851;VT=INDEL";


@BeforeAll
Expand All @@ -56,15 +54,15 @@ public static void initializeBinfile() throws Exception {

@Test
public void test_2a_variantFromFile_1_WasLoaded() {
String[] data = vmi.findBySingleVariantSpec("14,19038291,C,A", bucketCache);
String[] expecteds = {"AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=32694;AA=.|||;VT=SNP"};
String[] data = vmi.findBySingleVariantSpec("14,19038291,C,A,ABC,splice_region_variant", bucketCache);
String[] expecteds = {"Gene_with_variant=ABC;Variant_severity=LOW;Variant_consequence_calculated=splice_region_variant;Variant_class=SNV;Variant_frequency_in_gnomAD=0.0001578;Variant_frequency_as_text=Rare"};
assertEquals("The expected values were not found.", expecteds, data);
}

@Test
public void test_2b_variantFromFile_2_WasLoaded() {
String[] data = vmi.findBySingleVariantSpec("14,21089541,A,G", bucketCache);
String[] expecteds = {"AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.44000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18507;AA=A|||;VT=SNP"};
String[] data = vmi.findBySingleVariantSpec("14,21089541,A,G,DEF,missense_variant", bucketCache);
String[] expecteds = {"Gene_with_variant=DEF;Variant_severity=MODERATE;Variant_consequence_calculated=missense_variant;Variant_class=SNV;Variant_frequency_in_gnomAD=4.599e-05;Variant_frequency_as_text=Rare"};
assertEquals("The expected values were not found.", expecteds, data);
}

Expand All @@ -77,12 +75,12 @@ public void test_2c_variantFromFile_3_WasNotLoaded() {

@Test
public void test_4_MultipleVariantSpec() {
List<String> variants = List.of("14,19038291,C,A", "14,21089541,A,G");
List<String> variants = List.of("14,19038291,C,A,ABC,splice_region_variant", "14,21089541,A,G,DEF,missense_variant");
Map<String,String[]> expectedResult = Map.of(
"14,19038291,C,A"
, new String[]{"AC=14;AF=2.79553e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=1.09000e-02;AFR_AF=0.00000e+00;AMR_AF=4.30000e-03;SAS_AF=0.00000e+00;DP=32694;AA=.|||;VT=SNP"}
,"14,21089541,A,G"
,new String[]{"AC=20;AF=3.99361e-03;NS=2504;AN=5008;EAS_AF=0.00000e+00;EUR_AF=0.00000e+00;AFR_AF=1.44000e-02;AMR_AF=1.40000e-03;SAS_AF=0.00000e+00;DP=18507;AA=A|||;VT=SNP"});
"14,19038291,C,A,ABC,splice_region_variant"
, new String[]{"Gene_with_variant=ABC;Variant_severity=LOW;Variant_consequence_calculated=splice_region_variant;Variant_class=SNV;Variant_frequency_in_gnomAD=0.0001578;Variant_frequency_as_text=Rare"}
,"14,21089541,A,G,DEF,missense_variant"
,new String[]{"Gene_with_variant=DEF;Variant_severity=MODERATE;Variant_consequence_calculated=missense_variant;Variant_class=SNV;Variant_frequency_in_gnomAD=4.599e-05;Variant_frequency_as_text=Rare"});
Map<String, String[]>[] data = new Map[] {vmi.findByMultipleVariantSpec(variants)};

assertEquals("Wrong number of records in response.", data[0].size(), 2);
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