Peak calling to dev

bin/1.1_footprint_extraction/footprints_extraction.py

@@ -48,13 +48,12 @@ def parse_args():
 
 	return args
 
-#this function is currently unused, but may be used in the future version
-#if there are several files producing by this script, the directory containing these files is useful to have
 #this function checks if the directory for the output files exists and if not, the new directory with default name will be created
+#the input for this function is a directory to check
 def check_directory(directory):
 	if not os.path.exists(directory):
 		os.makedirs(directory)
-		print('The new directory ' + directory + ' was created!')
+		logger.info('The new directory ' + directory + ' was created!')
 
 #check if the file to remove exists and if so, delete it
 #if the file does not exist, nothing happens
@@ -96,6 +95,9 @@ def make_bed_dictionary(bed_file):
 					for i in range(3, len(bed_line_array)):
 						value.append(bed_line_array[i]) 
 
+					if not value: #if there is no bonus information in the original bed file, add a "." to the coulmn in the output bed file
+						value = ["."]
+
 					bed_dictionary[key] = value
 				else: #this is not a bed file, force exit
 					logger.info('Error: please make sure the input bed file has a right format, the problem occured on the line ' + bed_line)
@@ -315,6 +317,9 @@ def write_to_bed_file(all_footprints, sorted_output_file_name):
 
 	#extract the name of directory where we want to save the file
 	output_directory = os.path.dirname(sorted_output_file_name)
+	#check if there is a directory provided
+	if output_directory:
+		check_directory(output_directory)
 
 	#make sure the file is in .bed format
 	output_name = "not_sorted_" + os.path.splitext(os.path.basename(sorted_output_file_name))[0] + ".bed"