Fix splice site detection (#1881)

* treat splice sites in lowercase when pulling from config * compare splice sites in lowercase
GMOD · Apr 21, 2018 · 203444e · 203444e
1 parent 01a7c1c
commit 203444e
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Showing 3 changed files with 16 additions and 8 deletions.
diff --git a/grails-app/services/org/bbop/apollo/ConfigWrapperService.groovy b/grails-app/services/org/bbop/apollo/ConfigWrapperService.groovy
@@ -50,11 +50,19 @@ class ConfigWrapperService {
     }
 
     List<String> getSpliceDonorSites(){
-        return grailsApplication.config.apollo.splice_donor_sites
+        List<String> sites = new ArrayList<String>()
+        grailsApplication.config.apollo.splice_donor_sites.each {
+            sites.add(it.toLowerCase())
+        }
+        return sites
     }
 
     List<String> getSpliceAcceptorSites(){
-        return grailsApplication.config.apollo.splice_acceptor_sites
+        List<String> sites = new ArrayList<String>()
+        grailsApplication.config.apollo.splice_acceptor_sites.each {
+            sites.add(it.toLowerCase())
+        }
+        return sites
     }
 
     int getDefaultMinimumIntronSize() {

diff --git a/grails-app/services/org/bbop/apollo/ExonService.groovy b/grails-app/services/org/bbop/apollo/ExonService.groovy
@@ -263,7 +263,7 @@ class ExonService {
             }
             String seq = residues.substring(coordinate, coordinate + 2);
 
-            if (SequenceTranslationHandler.getSpliceDonorSites().contains(seq)) {
+            if (SequenceTranslationHandler.getSpliceDonorSites().contains(seq.toLowerCase())) {
                 if (exon.getFeatureLocation().getStrand() == -1) {
                     setExonBoundaries(exon,featureService.convertLocalCoordinateToSourceCoordinate(gene,coordinate)+1,exon.getFeatureLocation().getFmax())
                 } else {
@@ -292,7 +292,7 @@ class ExonService {
             String seq = residues.substring(coordinate, coordinate + 2);
 
 //            log.debug "seq ${seq} in ${SequenceTranslationHandler.spliceDonorSites}"
-            if (SequenceTranslationHandler.getSpliceDonorSites().contains(seq)) {
+            if (SequenceTranslationHandler.getSpliceDonorSites().contains(seq.toLowerCase())) {
                 if (exon.getStrand() == -1) {
                     setExonBoundaries(exon, featureService.convertLocalCoordinateToSourceCoordinate(gene,coordinate) + 1, exon.getFmax());
                 } else {
@@ -334,7 +334,7 @@ class ExonService {
                 throw new AnnotationException("Cannot set to upstream acceptor - will overlap previous exon");
             }
             String seq = residues.substring(coordinate, coordinate + 2);
-            if (SequenceTranslationHandler.getSpliceAcceptorSites().contains(seq)) {
+            if (SequenceTranslationHandler.getSpliceAcceptorSites().contains(seq.toLowerCase())) {
                 if (exon.getStrand() == -1) {
                     setExonBoundaries(exon, exon.getFmin(), featureService.convertLocalCoordinateToSourceCoordinate(gene,coordinate) - 1);
                 } else {
@@ -360,7 +360,7 @@ class ExonService {
                 throw new AnnotationException("Cannot set to downstream acceptor - will remove exon");
             }
             String seq = residues.substring(coordinate, coordinate + 2);
-            if (SequenceTranslationHandler.getSpliceAcceptorSites().contains(seq)) {
+            if (SequenceTranslationHandler.getSpliceAcceptorSites().contains(seq.toLowerCase())) {
                 if (exon.getStrand() == -1) {
                     setExonBoundaries(exon, exon.getFmin(), featureService.convertLocalCoordinateToSourceCoordinate(gene,coordinate) - 1);
                 } else {

diff --git a/grails-app/services/org/bbop/apollo/NonCanonicalSplitSiteService.groovy b/grails-app/services/org/bbop/apollo/NonCanonicalSplitSiteService.groovy
@@ -125,7 +125,7 @@ class NonCanonicalSplitSiteService {
                         String acceptorSpliceSiteSequence = residues.substring(local1,local2)
                         acceptorSpliceSiteSequence=transcript.getStrand()==-1?acceptorSpliceSiteSequence.reverse():acceptorSpliceSiteSequence
                         log.debug "acceptor ${local1} ${local2} ${acceptorSpliceSiteSequence} ${acceptor}"
-                        if(acceptorSpliceSiteSequence==acceptor)
+                        if(acceptorSpliceSiteSequence.toLowerCase() == acceptor)
                             validThreePrimeSplice=true
                         else
                             threePrimeSpliceSitePosition = exon.getStrand() == -1 ? local1 : local2;
@@ -135,7 +135,7 @@ class NonCanonicalSplitSiteService {
                         String donorSpliceSiteSequence = residues.substring(local3,local4)
                         donorSpliceSiteSequence=transcript.getStrand()==-1?donorSpliceSiteSequence.reverse():donorSpliceSiteSequence
                         log.debug "donor ${local3} ${local4} ${donorSpliceSiteSequence} ${donor}"
-                        if(donorSpliceSiteSequence==donor)
+                        if(donorSpliceSiteSequence.toLowerCase() == donor)
                             validFivePrimeSplice=true
                         else
                             fivePrimeSpliceSitePosition = exon.getStrand() == -1 ? local3 : local4;