enable disabling of calculating non_canonical splice sites (#2510)

* enable disabling of calucating non_canonical splice sites * added a bit of doc to support this
GMOD · Aug 31, 2020 · f27376b · f27376b
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diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,4 +1,13 @@
 
+
+## 2.6.2
+
+Features
+
+- Add option to suppress calculation of non-canonical splice site [2509](https://github.com/GMOD/Apollo/issues/2509).
+
+
+
 ## 2.6.1
 
 Infrastructure Changes

diff --git a/docker-files/createenv.sh b/docker-files/createenv.sh
@@ -36,6 +36,7 @@ echo "export WEBAPOLLO_FEATURE_HAS_DBXREFS=$WEBAPOLLO_FEATURE_HAS_DBXREFS" >> $S
 echo "export WEBAPOLLO_FEATURE_HAS_ATTRS=$WEBAPOLLO_FEATURE_HAS_ATTRS" >>$SET_ENV_FILE
 echo "export WEBAPOLLO_FEATURE_HAS_PUBMED=$WEBAPOLLO_FEATURE_HAS_PUBMED" >>$SET_ENV_FILE
 echo "export WEBAPOLLO_FEATURE_HAS_GO=$WEBAPOLLO_FEATURE_HAS_GO" >>$SET_ENV_FILE
+echo "export WEBAPOLLO_CALCULATE_NON_CANONICAL_SPLICE_SITES=$WEBAPOLLO_CALCULATE_NON_CANONICAL_SPLICE_SITES" >>$SET_ENV_FILE
 echo "export WEBAPOLLO_FEATURE_HAS_COMMENTS=$WEBAPOLLO_FEATURE_HAS_COMMENTS" >>$SET_ENV_FILE
 echo "export WEBAPOLLO_FEATURE_HAS_STATUS=$WEBAPOLLO_FEATURE_HAS_STATUS" >> $SET_ENV_FILE
 echo "export WEBAPOLLO_TRANSLATION_TABLE=$WEBAPOLLO_TRANSLATION_TABLE" >> $SET_ENV_FILE

diff --git a/docker-files/docker-apollo-config.groovy b/docker-files/docker-apollo-config.groovy
@@ -105,7 +105,8 @@ apollo {
     feature_has_dbxrefs = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_DBXREFS",true)
     feature_has_attributes = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_ATTRS",true)
     feature_has_pubmed_ids = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_PUBMED",true)
-    feature_has_go_ids = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_GO",true)
+    feature_has_go_ids =checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_GO",true)
+    calculate_non_canonical_splice_sites = checkBooleanEnvironment("WEBAPOLLO_CALCULATE_NON_CANONICAL_SPLICE_SITES",true)
     feature_has_comments = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_COMMENTS",true)
     feature_has_status = checkBooleanEnvironment("WEBAPOLLO_FEATURE_HAS_STATUS",true)
     translation_table = "/config/translation_tables/ncbi_" + (System.getenv("WEBAPOLLO_TRANSLATION_TABLE") ?: "1") + "_translation_table.txt"

diff --git a/docs/Configure.md b/docs/Configure.md
@@ -76,6 +76,12 @@ grails {
 }
 ```
 
+### Suppress calculation of non-canonical splice sites
+
+By default we calculate non-canonical splice sites.  For some organisms this is undesirable.
+
+    apollo.calculate_non_canonical_splice_sites = false 
+
 ### Count annotations
 
 By default annotations are counted, but in some cases this can be come prohibitive for performance if a lot of annotations. 

diff --git a/grails-app/conf/Config.groovy b/grails-app/conf/Config.groovy
@@ -216,6 +216,7 @@ apollo {
     is_partial_translation_allowed = false // unused so far
     export_subfeature_attrs = false
     store_orig_id = true // sets the orig_id to the original evidence id when first created
+    calculate_non_canonical_splice_sites = true
 
     // used for uploading
 //    common_data_directory = "/opt/apollo"

diff --git a/grails-app/services/org/bbop/apollo/ConfigWrapperService.groovy b/grails-app/services/org/bbop/apollo/ConfigWrapperService.groovy
@@ -164,4 +164,9 @@ class ConfigWrapperService {
       return grailsApplication.config.gff3.source
     }
 
+
+    boolean getCalculateNonCanonicalSpliceSites(){
+       return grailsApplication.config.apollo.calculate_non_canonical_splice_sites
+    }
+
 }
diff --git a/grails-app/services/org/bbop/apollo/NonCanonicalSplitSiteService.groovy b/grails-app/services/org/bbop/apollo/NonCanonicalSplitSiteService.groovy
@@ -10,7 +10,7 @@ import org.grails.plugins.metrics.groovy.Timed
 class NonCanonicalSplitSiteService {
 
     def featureRelationshipService
-    def exonService
+    def configWrapperService
     def transcriptService
     def featureService
     def sequenceService
@@ -142,15 +142,17 @@ class NonCanonicalSplitSiteService {
                     }
                 }
             }
-            if (!validFivePrimeSplice && fivePrimeSpliceSitePosition != -1) {
-                def loc=fivePrimeSpliceSitePosition+transcript.fmin
-                log.debug "adding a noncanonical five prime splice site at ${fivePrimeSpliceSitePosition} ${loc}"
-                addNonCanonicalFivePrimeSpliceSite(transcript,createNonCanonicalFivePrimeSpliceSite(transcript, loc));
-            }
-            if (!validThreePrimeSplice && threePrimeSpliceSitePosition != -1) {
-                def loc=threePrimeSpliceSitePosition+transcript.fmin
-                log.debug "adding a noncanonical three prime splice site at ${threePrimeSpliceSitePosition} ${loc}"
-                addNonCanonicalThreePrimeSpliceSite(transcript,createNonCanonicalThreePrimeSpliceSite(transcript, loc));
+            if(configWrapperService.getCalculateNonCanonicalSpliceSites()){
+                if (!validFivePrimeSplice && fivePrimeSpliceSitePosition != -1) {
+                    def loc=fivePrimeSpliceSitePosition+transcript.fmin
+                    log.debug "adding a noncanonical five prime splice site at ${fivePrimeSpliceSitePosition} ${loc}"
+                    addNonCanonicalFivePrimeSpliceSite(transcript,createNonCanonicalFivePrimeSpliceSite(transcript, loc));
+                }
+                if (!validThreePrimeSplice && threePrimeSpliceSitePosition != -1) {
+                    def loc=threePrimeSpliceSitePosition+transcript.fmin
+                    log.debug "adding a noncanonical three prime splice site at ${threePrimeSpliceSitePosition} ${loc}"
+                    addNonCanonicalThreePrimeSpliceSite(transcript,createNonCanonicalThreePrimeSpliceSite(transcript, loc));
+                }
             }
         }
 
@@ -190,7 +192,7 @@ class NonCanonicalSplitSiteService {
      *
      * @param nonCanonicalThreePrimeSpliceSite - Non canonical 3' splice site to be added
      */
-    public void addNonCanonicalThreePrimeSpliceSite(Transcript transcript,NonCanonicalThreePrimeSpliceSite nonCanonicalThreePrimeSpliceSite) {
+    void addNonCanonicalThreePrimeSpliceSite(Transcript transcript,NonCanonicalThreePrimeSpliceSite nonCanonicalThreePrimeSpliceSite) {
 
         // add non canonical 3' splice site
         FeatureRelationship fr = new FeatureRelationship(

diff --git a/sample-h2-apollo-config.groovy b/sample-h2-apollo-config.groovy
@@ -65,6 +65,7 @@ environments {
 //    gff3.source = "MyOrg" // also for GPAD export
 //    only_owners_delete = true
 //    common_data_directory = "/opt/temporary/apollo"
+//    calculate_non_canonical_splice_sites = false
 //    store_orig_id = false
 //    count_annotations = false
 //    fa_to_twobit_exe = "/usr/local/bin/blat" // get form https://genome.ucsc.edu/goldenPath/help/blatSpec.html

diff --git a/sample-mysql-apollo-config.groovy b/sample-mysql-apollo-config.groovy
@@ -66,6 +66,7 @@ environments {
 //    common_data_directory = "/opt/temporary/apollo"
 //    store_orig_id = false
 //    count_annotations = false
+//    calculate_non_canonical_splice_sites = false
 //    fa_to_twobit_exe = "/usr/local/bin/faToTwoBit" // get from // https://genome.ucsc.edu/goldenPath/help/blatSpec.html
 //    sequence_search_tools {
 //        blat_nuc {

diff --git a/sample-postgres-apollo-config.groovy b/sample-postgres-apollo-config.groovy
@@ -109,6 +109,7 @@ environments {
 //    gff3.source = "MyOrg" // also for GPAD export
 //    only_owners_delete = true
 //    common_data_directory = "/opt/temporary/apollo"
+//    calculate_non_canonical_splice_sites = false
 //    count_annotations = false
 //    store_orig_id = false
 //    fa_to_twobit_exe = "/usr/local/bin/faToTwoBit" // get from // https://genome.ucsc.edu/goldenPath/help/blatSpec.html