Tries to Fix #18

loosolab · Jan 3, 2019 · f3b93f2 · f3b93f2
1 parent e1db4c2
commit f3b93f2
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Showing 3 changed files with 5 additions and 3 deletions.
diff --git a/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py b/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py
@@ -67,13 +67,15 @@ def reformat_to_gff(self, activity, release):
 
     @staticmethod
     def generate_additional_information(gene_id, activity):
-
+        # helper method to concat activity information to string
+        print(gene_id)
         if gene_id.startswith("ID=regulatory_region:"):
-            gene_id = 'ID "'+gene_id.split(':')[1]+'"'
+            gene_id = 'gene_id "'+gene_id.split(':')[1]+'"'
+        elif gene_id.startswith("ID=E"):
+            gene_id = 'gene_id "'+gene_id.split('=')[1]+'"'
 
         activity_string = 'activity "'+', '.join(activity)+'"'
 
-        # helper method to concat activity information to string
         return gene_id+'; '+activity_string
 
     def generate_activity_list(self, activity, index):

diff --git a/bin/3.1_create_gtf/Modules/ucsc/bigBedToBed b/bin/3.1_create_gtf/Modules/ucsc/bigBedToBed
diff --git a/...vity/Aorta/homo_sapiens.GRCh38.Aorta.Regulatory_Build.regulatory_activity.20161111.gff.gz b/...vity/Aorta/homo_sapiens.GRCh38.Aorta.Regulatory_Build.regulatory_activity.20161111.gff.gz