adding a validation while printing to the output file. If there are p…

…roblems with start/end positions or max_pos, the footprint will not be written to the output file

bin/1.1_footprint_extraction/footprints_extraction.py

@@ -529,11 +529,18 @@ def write_to_bed_file(all_footprints, sorted_output_file_name):
 
 	#write each footprint line for line to the output file
 	for footprint in all_footprints:
-		#if footprint[1]['start'] >= footprint[1]['end']:
-		#	print(footprint)
-		#if footprint[1]['max_pos'] == 0:
-		#	print(footprint)
-		output_file.write('\t'.join([footprint[1]['chromosom'], str(footprint[1]['start']), str(footprint[1]['end']), footprint[0], str(round(footprint[1]['score'], 6)), '.', str(footprint[1]['len']), str(footprint[1]['max_pos']), ';'.join(footprint[1]['bonus'])]) + '\n')
+		#validation of the footprints, if there is a problem with some of them, write which one it is
+		#first check the start and end positions
+		if footprint[1]['start'] >= footprint[1]['end']:
+			logger.info("The problem occured with start and end positions. This footprint will not be printed to the output file:")
+			logger.info(footprint)
+		#then check the max_pos
+		elif footprint[1]['max_pos'] == 0:
+			logger.info("The problem occured with max_pos of the footprint. This footprint will not be printed to the output file:")
+			logger.info(footprint)
+		#otherwise everything is fine, write to the output
+		else:
+			output_file.write('\t'.join([footprint[1]['chromosom'], str(footprint[1]['start']), str(footprint[1]['end']), footprint[0], str(round(footprint[1]['score'], 6)), '.', str(footprint[1]['len']), str(footprint[1]['max_pos']), ';'.join(footprint[1]['bonus'])]) + '\n')
 
 	output_file.close()