diff --git a/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py b/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py index 9e7b223..98f88da 100644 --- a/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py +++ b/bin/3.1_create_gtf/Modules/Ensembl/GTFGen.py @@ -51,7 +51,7 @@ def reformat_to_gff(self, activity, release): # Add RegBuild_ + release templist.append("RegBuild_"+release) # Add Description from Description in last ; separated segment - templist.append(splitted_additional[4].split("=")[1].lower()) + templist.append(splitted_additional[4].split("=")[1].lower().replace(' ', '_')) # Add Start / End Data from original templist.extend(splitted[3:5]) # Add Score, Strand and Frame Data @@ -68,7 +68,6 @@ 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 = 'gene_id "'+gene_id.split(':')[1]+'"' elif gene_id.startswith("ID=E"): diff --git a/bin/3.1_create_gtf/Modules/ucsc/ucsc.py b/bin/3.1_create_gtf/Modules/ucsc/ucsc.py index da086ef..66eb2ac 100644 --- a/bin/3.1_create_gtf/Modules/ucsc/ucsc.py +++ b/bin/3.1_create_gtf/Modules/ucsc/ucsc.py @@ -41,7 +41,7 @@ def read_gff_to_gtf(self): sequence = [] sequence.append(row[0]) sequence.append("UCSC") - sequence.append(row[3].lower()) + sequence.append(row[3].lower().replace(' ', '_')) sequence.append(row[1]) sequence.append(row[2]) sequence.append(".")