write each transcript with the corresponding gene in the output file

find_exons.py

@@ -42,7 +42,7 @@ 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', 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)
+	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)
 
 	#all other arguments are optional
 	parser.add_argument('--genes_file', help='names of genes of interest')
@@ -81,32 +81,32 @@ def check_existing_input_files(args):
 		print('please make sure the .gtf file with exons 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
-
+	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
 		else:
-			print('please provide a path to a file with genes of interest')
-			sys.exit()
+			print('working with file of genes')
+			#there is a file with list of genes. Extract them and return in an array
+			genes = []
+			with open(args.genes_of_interest[0]) 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()
+			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
 
-	return args.genes
+	return genes_of_interest
 
 def procede_gtf_files(gtf_genes, gtf_exons, genes_of_interest, exact):
 
@@ -314,7 +314,7 @@ def plot_and_output(all_genes, output_directory, gene_groups):
 				score = "%.2f" % round((sum_length * 100)/all_genes[gene]['gene_length'], 2)
 				gene_transcript_name = gene + "_" + transcript_name
 				genes_with_transcript_names[gene_transcript_name] = genes_with_transcript_names.get(transcript_name, {})
-				genes_with_transcript_names[gene_transcript_name] = {'gene': gene, 'sum_length': sum_length, 'gene_length': all_genes[gene]['gene_length'], 'score': score}
+				genes_with_transcript_names[gene_transcript_name] = {'gene': gene, 'sum_length': sum_length, 'gene_length': all_genes[gene]['gene_length'], 'score': score} #anzahl von exons
 				transcript_name = sorted_exons[i][5]
 				sum_length = sorted_exons[i][0]
 			else: #this is still the same transcript name