check for the inputs

find_exons.py

@@ -39,9 +39,10 @@ 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('--gene_list', help='names of genes of interest', required=True)
+	required_arguments.add_argument('--genes_of_interest', nargs='*', dest='genes', help='enter a list of genes of interest or type file and enter a path to the file with genes of interest with the optional argument --genes_file', default=['file'], required=True)
 
 	#all other arguments are optional
+	parser.add_argument('--genes_file', help='names of genes of interest')
 	parser.add_argument('--output_directory',  default='output', const='output', nargs='?', help='output directory, by default ./output/')
 	parser.add_argument('--silent', action='store_true', help='while working with data write the information only into ./call_peaks_log.txt')
 	args = parser.parse_args()
@@ -67,26 +68,47 @@ def get_name_from_path(full_path):
 def check_existing_input_files(args):
 
 	if not os.path.isfile(args.gtf_genes):
-		#logger.info('please make sure the both files with conditions to compare exist')
 		print('please make sure the .gtf file with genes exists')
 		sys.exit()
 
 	if not os.path.isfile(args.gtf_exons):
-		#logger.info('please make sure the both files with conditions to compare exist')
 		print('please make sure the .gtf file with exons exists')
 		sys.exit()
 
-	if not os.path.isfile(args.gene_list):
-		print('please make sure the file with genes of interest exists')
-		sys.exit()
+	if len(args.genes) == 1 and args.genes[0] == "file":
+		if args.genes_file != None:
+			if not os.path.isfile(args.genes_file):
+				print('please make sure the file with genes of interest exists')
+				sys.exit()
+			else:
+				#there is a file with list of genes. Extract them and return in an array
+				genes = []
+				with open(args.genes_file) as genes_file:
+					for line in genes_file:
+						line_array = re.split(r'\t', line.rstrip('\n'))
+						for gene in line_array:
+							if ' ' in gene:
+								print('please make sure that genes in the file with genes of interest are separated with tabs or are written each on a new line')
+								sys.exit()
+							else:
+								genes.append(gene)
+
+				genes_file.close()
+				args.genes = genes
+
+		else:
+			print('please provide a path to a file with genes of interest')
+			sys.exit()
+
+	return args.genes
 
 def main():
 
 	start = time.time()
 
 	args = parse_args()
 
-	check_existing_input_files(args)
+	args.genes = check_existing_input_files(args)
 
 	#check if there is an existing directory that user gave as input, otherwise create this directory from the path provided from the user
 	check_directory(args.output_directory)