Add subRVIS gene demain / exon filters - issue 2560

nickzren · Aug 2, 2017 · 13835ef · 13835ef
1 parent 198a06d
commit 13835ef
Show file tree

Hide file tree

Showing 4 changed files with 106 additions and 9 deletions.
diff --git a/src/main/java/function/annotation/base/AnnotatedVariant.java b/src/main/java/function/annotation/base/AnnotatedVariant.java
@@ -1,5 +1,6 @@
 package function.annotation.base;
 
+import function.external.bis.BisOutput;
 import function.external.denovo.DenovoDB;
 import function.external.denovo.DenovoDBCommand;
 import function.external.evs.Evs;
@@ -63,6 +64,7 @@ public class AnnotatedVariant extends Variant {
     private KnownVarOutput knownVarOutput;
     private String rvisStr;
     private SubRvisOutput subRvisOutput;
+    private BisOutput bisOutput;
     private Genomes genomes;
     private String mgiStr;
     private DenovoDB denovoDB;
@@ -161,10 +163,6 @@ public void initExternalData() {
             rvisStr = RvisManager.getLine(getGeneName());
         }
 
-        if (SubRvisCommand.isIncludeSubRvis) {
-            subRvisOutput = new SubRvisOutput(getGeneName(), getChrStr(), getStartPosition());
-        }
-
         if (MgiCommand.isIncludeMgi) {
             mgiStr = MgiManager.getLine(getGeneName());
         }
@@ -176,7 +174,8 @@ public void initExternalData() {
 
     public boolean isValid() {
         return isValid
-                & isTrapValid();
+                && isTrapValid()
+                && isSubRVISValid();
     }
 
     private boolean isTrapValid() {
@@ -187,17 +186,35 @@ private boolean isTrapValid() {
                 trapScore = TrapManager.getScore(chrStr, getStartPosition(), allele, geneName);
             }
 
-            if (effect.equals("SYNONYMOUS_CODING")
-                    || effect.equals("INTRON_EXON_BOUNDARY")
-                    || effect.equals("INTRON")) {
-                // filter only apply to SYNONYMOUS_CODING, INTRON_EXON_BOUNDARY and INTRONIC variants
+            if (effect.equals("missense_variant")
+                    || effect.equals("intron_variant")) {
+                // filter only apply to missense_variant and intron_variant variants
                 return TrapCommand.isTrapScoreValid(trapScore);
             }
         }
 
         return true;
     }
 
+    // init sub rvis score base on most damaging gene and applied filter
+    private boolean isSubRVISValid() {
+        if (SubRvisCommand.isIncludeSubRvis) {
+            subRvisOutput = new SubRvisOutput(getGeneName(), getChrStr(), getStartPosition());
+
+            // sub rvis filters will only apply missense variants
+            if (effect.startsWith("missense_variant")) {
+                return SubRvisCommand.isSubRVISDomainScoreValid(subRvisOutput.getDomainScore())
+                        && SubRvisCommand.isSubRVISDomainOEratioValid(subRvisOutput.getDomainOEratio())
+                        && SubRvisCommand.isSubRVISExonScoreValid(subRvisOutput.getExonScore())
+                        && SubRvisCommand.isSubRVISExonOEratioValid(subRvisOutput.getExonOEratio());
+            } else {
+                return true;
+            }
+        }
+
+        return true;
+    }
+
     public void getAnnotationData(StringBuilder sb) {
         sb.append(getStableId()).append(",");
         sb.append(hasCCDS).append(",");

diff --git a/src/main/java/function/external/subrvis/SubRvisCommand.java b/src/main/java/function/external/subrvis/SubRvisCommand.java
@@ -1,10 +1,54 @@
 package function.external.subrvis;
 
+import global.Data;
+
 /**
  *
  * @author nick
  */
 public class SubRvisCommand {
+
     public static boolean isListSubRvis = false;
     public static boolean isIncludeSubRvis = false;
+
+    public static float subRVISDomainScorePercentile = Data.NO_FILTER;
+    public static float subRVISDomainOEratioPercentile = Data.NO_FILTER;
+    public static float subRVISExonScorePercentile = Data.NO_FILTER;
+    public static float subRVISExonOEratioPercentile = Data.NO_FILTER;
+
+    public static boolean isSubRVISDomainScoreValid(float value) {
+        if (subRVISDomainScorePercentile == Data.NO_FILTER) {
+            return true;
+        }
+
+        return value <= subRVISDomainScorePercentile
+                || value == Data.FLOAT_NA;
+    }
+
+    public static boolean isSubRVISDomainOEratioValid(float value) {
+        if (subRVISDomainOEratioPercentile == Data.NO_FILTER) {
+            return true;
+        }
+
+        return value <= subRVISDomainOEratioPercentile
+                || value == Data.FLOAT_NA;
+    }
+
+    public static boolean isSubRVISExonScoreValid(float value) {
+        if (subRVISExonScorePercentile == Data.NO_FILTER) {
+            return true;
+        }
+
+        return value <= subRVISExonScorePercentile
+                || value == Data.FLOAT_NA;
+    }
+
+    public static boolean isSubRVISExonOEratioValid(float value) {
+        if (subRVISExonOEratioPercentile == Data.NO_FILTER) {
+            return true;
+        }
+
+        return value <= subRVISExonOEratioPercentile
+                || value == Data.FLOAT_NA;
+    }
 }
diff --git a/src/main/java/function/external/subrvis/SubRvisOutput.java b/src/main/java/function/external/subrvis/SubRvisOutput.java
@@ -38,6 +38,22 @@ public SubRvisOutput(String geneName, String chr, int pos) {
         }
     }
 
+    public float getDomainScore() {
+        return domainScore;
+    }
+
+    public float getDomainOEratio() {
+        return domainOEratio;
+    }
+
+    public float getExonScore() {
+        return exonScore;
+    }
+
+    public float getExonOEratio() {
+        return exonOEratio;
+    }
+
     @Override
     public String toString() {
         StringBuilder sb = new StringBuilder();

diff --git a/src/main/java/function/variant/base/VariantLevelFilterCommand.java b/src/main/java/function/variant/base/VariantLevelFilterCommand.java
@@ -150,6 +150,26 @@ public static void initOptions(Iterator<CommandOption> iterator)
                     GenomesCommand.maxGenomesAF = getValidFloat(option);
                     GenomesCommand.isInclude1000Genomes = true;
                     break;
+                case "--sub-rvis-domain-score-percentile":
+                    checkValueValid(100, 0, option);
+                    SubRvisCommand.subRVISDomainScorePercentile = getValidFloat(option);
+                    SubRvisCommand.isIncludeSubRvis = true;
+                    break;
+                case "--sub-rvis-domain-oeratio-percentile":
+                    checkValueValid(100, 0, option);
+                    SubRvisCommand.subRVISDomainOEratioPercentile = getValidFloat(option);
+                    SubRvisCommand.isIncludeSubRvis = true;
+                    break;
+                case "--sub-rvis-exon-score-percentile":
+                    checkValueValid(100, 0, option);
+                    SubRvisCommand.subRVISExonScorePercentile = getValidFloat(option);
+                    SubRvisCommand.isIncludeSubRvis = true;
+                    break;
+                case "--sub-rvis-exon-oeratio-percentile":
+                    checkValueValid(100, 0, option);
+                    SubRvisCommand.subRVISExonOEratioPercentile = getValidFloat(option);
+                    SubRvisCommand.isIncludeSubRvis = true;
+                    break;
                 case "--include-evs":
                     EvsCommand.isIncludeEvs = true;
                     break;