diff --git a/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py b/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py index ca57aa8..9e7b223 100644 --- 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 old mode 100644 new mode 100755 diff --git a/bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/Aorta/homo_sapiens.GRCh38.Aorta.Regulatory_Build.regulatory_activity.20161111.gff.gz b/bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/Aorta/homo_sapiens.GRCh38.Aorta.Regulatory_Build.regulatory_activity.20161111.gff.gz index 1afc777..b1dab9f 100644 Binary files a/bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/Aorta/homo_sapiens.GRCh38.Aorta.Regulatory_Build.regulatory_activity.20161111.gff.gz and b/bin/3.1_create_gtf/data/EnsemblData/release-94/homo_sapiens/activity/Aorta/homo_sapiens.GRCh38.Aorta.Regulatory_Build.regulatory_activity.20161111.gff.gz differ