added bis score to all variant based output and added relevant filters

nickzren · Aug 2, 2017 · fcabd95 · fcabd95
1 parent 13835ef
commit fcabd95
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Showing 3 changed files with 87 additions and 3 deletions.
diff --git a/src/main/java/function/annotation/base/AnnotatedVariant.java b/src/main/java/function/annotation/base/AnnotatedVariant.java
@@ -1,5 +1,7 @@
 package function.annotation.base;
 
+import function.external.bis.BisCommand;
+import function.external.bis.BisGene;
 import function.external.bis.BisOutput;
 import function.external.denovo.DenovoDB;
 import function.external.denovo.DenovoDBCommand;
@@ -175,7 +177,8 @@ public void initExternalData() {
     public boolean isValid() {
         return isValid
                 && isTrapValid()
-                && isSubRVISValid();
+                && isSubRVISValid()
+                && isBisValid();
     }
 
     private boolean isTrapValid() {
@@ -202,7 +205,7 @@ private boolean isSubRVISValid() {
             subRvisOutput = new SubRvisOutput(getGeneName(), getChrStr(), getStartPosition());
 
             // sub rvis filters will only apply missense variants
-            if (effect.startsWith("missense_variant")) {
+            if (effect.equals("missense_variant")) {
                 return SubRvisCommand.isSubRVISDomainScoreValid(subRvisOutput.getDomainScore())
                         && SubRvisCommand.isSubRVISDomainOEratioValid(subRvisOutput.getDomainOEratio())
                         && SubRvisCommand.isSubRVISExonScoreValid(subRvisOutput.getExonScore())
@@ -214,7 +217,33 @@ private boolean isSubRVISValid() {
 
         return true;
     }
-
+
+    // init bis score base on most damaging gene and applied filter
+    private boolean isBisValid() {
+        if (BisCommand.isIncludeBis) {
+            bisOutput = new BisOutput(getGeneName(), getChrStr(), getStartPosition());
+
+            // bis filters will only apply missense variants
+            if (effect.equals("missense_variant")) {
+                BisGene geneDomain = bisOutput.getGeneDomain();
+                BisGene geneExon = bisOutput.getGeneExon();
+
+                return BisCommand.isBisDomainScore0005Valid(geneDomain == null ? Data.FLOAT_NA : geneDomain.getScore0005())
+                        && BisCommand.isBisDomainScore0001Valid(geneDomain == null ? Data.FLOAT_NA : geneDomain.getScore0001())
+                        && BisCommand.isBisDomainScore00005Valid(geneDomain == null ? Data.FLOAT_NA : geneDomain.getScore00005())
+                        && BisCommand.isBisDomainScore00001Valid(geneDomain == null ? Data.FLOAT_NA : geneDomain.getScore00001())
+                        && BisCommand.isBisExonScore0005Valid(geneExon == null ? Data.FLOAT_NA : geneExon.getScore0005())
+                        && BisCommand.isBisExonScore0001Valid(geneExon == null ? Data.FLOAT_NA : geneExon.getScore0001())
+                        && BisCommand.isBisExonScore00005Valid(geneExon == null ? Data.FLOAT_NA : geneExon.getScore00005())
+                        && BisCommand.isBisExonScore00001Valid(geneExon == null ? Data.FLOAT_NA : geneExon.getScore00001());
+            } else {
+                return true;
+            }
+        }
+
+        return true;
+    }
+
     public void getAnnotationData(StringBuilder sb) {
         sb.append(getStableId()).append(",");
         sb.append(hasCCDS).append(",");
@@ -296,6 +325,7 @@ public void getExternalData(StringBuilder sb) {
         sb.append(get1000Genomes());
         sb.append(getRvis());
         sb.append(getSubRvis());
+        sb.append(getBis());
         sb.append(getGerpScore());
         sb.append(getTrapScore());
         sb.append(getMgi());
@@ -374,6 +404,14 @@ public String getSubRvis() {
         }
     }
 
+    public String getBis() {
+        if (BisCommand.isIncludeBis) {
+            return bisOutput.toString();
+        } else {
+            return "";
+        }
+    }
+
     public String get1000Genomes() {
         if (GenomesCommand.isInclude1000Genomes) {
             return genomes.toString();

diff --git a/src/main/java/function/variant/base/Output.java b/src/main/java/function/variant/base/Output.java
@@ -1,5 +1,6 @@
 package function.variant.base;
 
+import function.external.bis.BisManager;
 import function.external.denovo.DenovoDBManager;
 import function.external.evs.EvsManager;
 import function.external.exac.ExacManager;
@@ -56,6 +57,7 @@ public static String getExternalDataTitle() {
                 + GenomesManager.getTitle()
                 + RvisManager.getTitle()
                 + SubRvisManager.getTitle()
+                + BisManager.getTitle()
                 + GerpManager.getTitle()
                 + TrapManager.getTitle()
                 + MgiManager.getTitle()

diff --git a/src/main/java/function/variant/base/VariantLevelFilterCommand.java b/src/main/java/function/variant/base/VariantLevelFilterCommand.java
@@ -1,5 +1,6 @@
 package function.variant.base;
 
+import function.external.bis.BisCommand;
 import function.external.denovo.DenovoDBCommand;
 import function.external.evs.EvsCommand;
 import function.external.exac.ExacCommand;
@@ -170,6 +171,46 @@ public static void initOptions(Iterator<CommandOption> iterator)
                     SubRvisCommand.subRVISExonOEratioPercentile = getValidFloat(option);
                     SubRvisCommand.isIncludeSubRvis = true;
                     break;
+                case "--bis-domain-score-percentile-0.005":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisDomainScorePercentile0005 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
+                case "--bis-domain-score-percentile-0.001":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisDomainScorePercentile0001 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
+                case "--bis-domain-score-percentile-0.0005":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisDomainScorePercentile00005 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
+                case "--bis-domain-score-percentile-0.0001":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisDomainScorePercentile00001 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
+                case "--bis-exon-score-percentile-0.005":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisExonScorePercentile0005 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
+                case "--bis-exon-score-percentile-0.001":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisExonScorePercentile0001 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
+                case "--bis-exon-score-percentile-0.0005":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisExonScorePercentile00005 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
+                case "--bis-exon-score-percentile-0.0001":
+                    checkValueValid(100, 0, option);
+                    BisCommand.bisExonScorePercentile00001 = getValidFloat(option);
+                    BisCommand.isIncludeBis = true;
+                    break;
                 case "--include-evs":
                     EvsCommand.isIncludeEvs = true;
                     break;
@@ -197,6 +238,9 @@ public static void initOptions(Iterator<CommandOption> iterator)
                 case "--include-sub-rvis":
                     SubRvisCommand.isIncludeSubRvis = true;
                     break;
+                case "--include-bis":
+                    BisCommand.isIncludeBis = true;
+                    break;
 //                case "--include-1000-genomes":
 //                    GenomesCommand.isInclude1000Genomes = true;
 //                    break;