fixing the bug with the output directory name

bin/footprints_extraction.py

@@ -312,8 +312,15 @@ def find_peaks_from_bw(bed_dictionary, bw_file, window_length, step, percentage)
 #as input the dictionary with all footprints and the name for the output file are needed
 #the function outputs first an unsorted file and finally sorts it, removing the unsorted one
 def write_to_bed_file(all_footprints, sorted_output_file_name):
-	#save the output file in the working directory
-	output_file_name = "not_sorted_" + 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)
+
+	#make sure the file is in .bed format
+	output_name = "not_sorted_" + os.path.splitext(os.path.basename(sorted_output_file_name))[0] + ".bed"
+
+	#save the output file in the working directory or in the directory provided by the user
+	output_file_name = (os.path.join(output_directory, output_name))
 
 	#a header to know what is in the columns
 	header = ["#chr", "start", "end", "name", "score", "strand", "len", "max_pos", "bonus_info"]