Fixed: "No Module named bin Error" V2

bin/Modules/SaveResults.py

@@ -4,14 +4,14 @@
 
 class ResultSaver:
 
-    def __init__(self, results, organism, tissue):
+    def __init__(self, results, organism, tissue, wd):
 
         print("Save results to File !")
         self.path = ""
         if tissue:
-            self.path = os.path.join("./"+organism+"_filtered.gtf")
+            self.path = os.path.join(wd, "/"+organism+"_filtered.gtf")
         else:
-            self.path = os.path.join("./"+organism+".gtf")
+            self.path = os.path.join(wd, "./"+organism+".gtf")
 
         with open(self.path, "w") as file:
             write_it = csv.writer(file, delimiter='\t')

bin/RegGTFExtractor.py

@@ -25,17 +25,17 @@ def main_script(org, wd, tissuetype=None):
     ense = Ensembl(org, wd)
     print("Getting Unique Results")
     unique_filter = UniqueFilter(ense.get_gtf(), ucsc.get_gtf(), tissuetype)
-    ResultSaver(unique_filter.get_results(), org, tissuetype)
+    ResultSaver(unique_filter.get_results(), org, tissuetype, wd)
 
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='GTF-Generator from UCSC Table Browser and Ensembl Regulatory Build' )
     parser.add_argument('organism', help='Source organism [ homo_sapiens or mus_musculus ]', action='store', nargs='?', type=str)
     parser.add_argument('--tissue', help='Tissue- or Celltype(s)', action='store', nargs='*', type=str)
-    parser.add_argument('--wd', help='Working directory. default: "."', default=".", action='store', type=str)
+    parser.add_argument('--wd', help='Working directory. default: "."', action='store', nargs='*', type=str)
     args = vars(parser.parse_args())
     if args["organism"]:
-        #print(args["tissue"])
+        print("Working Dir: " + args["wd"])
         main_script(args["organism"], args["wd"], args["tissue"])
     else:
         print("No Arguments found -> See ./RegGTFExtractor.py -h for help.")