input genes of interest as a text file only and no more as list

find_exons.py

@@ -31,7 +31,7 @@ def parse_args():
 	required_arguments = parser.add_argument_group('required arguments')
 	required_arguments.add_argument('--gtf_genes', help='a .gtf file with genes', required=True)
 	required_arguments.add_argument('--gtf_exons', help='a .gtf file with exons', required=True)
-	required_arguments.add_argument('--genes_of_interest', nargs='*', dest='genes_of_interest', help='a .txt file or a list with genes one is interested in', required=True)
+	required_arguments.add_argument('--genes_of_interest', nargs='*', dest='genes_of_interest', help='a .txt file with genes of interest containing one columnt with gene names', required=True)
 
 	#all other arguments are optional
 	parser.add_argument('--output_directory',  default='output', const='output', nargs='?', help='output directory, by default ./output/')
@@ -46,16 +46,6 @@ def check_directory(directory):
 		os.makedirs(directory)
 		print('a new directory ' + directory + ' was created')
 
-def remove_file(file):
-	if os.path.isfile(file):
-		os.remove(file)
-
-def make_name_from_path(full_path, output_directory, ending):
-	return os.path.join(output_directory, get_name_from_path(full_path) + ending)
-
-def get_name_from_path(full_path):
-	return os.path.splitext(os.path.basename(full_path))[0]
-
 def check_existing_input_files(args):
 
 	print('checking the input files')
@@ -70,8 +60,9 @@ def check_existing_input_files(args):
 
 	if len(args.genes_of_interest) == 1:
 		if not os.path.isfile(args.genes_of_interest[0]):
-			print('working with one gene of interest')
-			genes_of_interest = args.genes_of_interest
+			#print('working with one gene of interest')
+			#genes_of_interest = args.genes_of_interest
+			print('please provide a file with genes of interest in .txt format containint one column with names of genes you are interested in')
 		else:
 			print('reading from the file with genes')
 			#there is a file with list of genes. Extract them and return in an array
@@ -90,8 +81,9 @@ def check_existing_input_files(args):
 			genes_of_interest = genes
 
 	else: #there is a list of genes of interest
-		print('working with a list of genes')
-		genes_of_interest = args.genes_of_interest
+		#print('working with a list of genes')
+		#genes_of_interest = args.genes_of_interest
+		print('please provide only one file with genes of interest')
 
 	return genes_of_interest