the structure is ready, this need to be adjusted to the data the foot…

…print_extraction parses

bin/1.1_footprint_extraction/footprints_extraction.py

@@ -280,6 +280,9 @@ def search_in_window(peak_footprints, footprint_count, chromosom, peak_start, pe
 #the output is the renewed dictionary containing only the best footprints for the output file
 def check_and_merge(peak_footprints, max_bp_between):
 	peak_footprints_new = {}
+	merged_footprints = {}
+
+	print(len(peak_footprints))
 
 	for footprint_to_check in peak_footprints.keys():
 		start_to_check = peak_footprints[footprint_to_check]['start']
@@ -291,38 +294,111 @@ def check_and_merge(peak_footprints, max_bp_between):
 
 			if start_to_check > peak_footprints[compared_footprint]['start'] and start_to_check - peak_footprints[compared_footprint]['end'] < max_bp_between:
 				#make compared_footprint longer
+				print()
+				print("footprint_to_check", footprint_to_check)
+				print(compared_footprint, " + ", footprint_to_check)
 				merge_footprints_left = False
 				break
 			elif end_to_check < peak_footprints[compared_footprint]['end'] and peak_footprints[compared_footprint]['start'] - end_to_check < max_bp_between:
 				#make footprint_to_check longer
+				print()
+				print("footprint_to_check", footprint_to_check)
+				print(footprint_to_check, " + ", compared_footprint)
 				merge_footprints_left = True
 				break
 
-		if merge_footprints_left: #if the merging left is enabled
-			#check if this footprint can be merged with the compared_footprint
-			#if compared footprint is not in peak_footprint_new.keys(), the next loop will check for this footprint. There is no need for doulbe check now
-			if start_to_check < peak_footprints[compared_footprint]['start'] and compared_footprint in peak_footprints_new.keys(): 
-				#update the start position
-				peak_footprints_new[compared_footprint]['start'] = start_to_check
-				#update the length
-				peak_footprints_new[compared_footprint]['len'] = peak_footprints[compared_footprint]['end'] - start_to_check
-				#update the score
-				peak_footprints_new[compared_footprint]['score'] = (peak_footprints[footprint_to_check]['score'] + peak_footprints[compared_footprint]['score']) / 2
-
-		elif merge_footprints_left == False: #otherwise merge right
-			#check if the merging is possible
-			if end_to_check > peak_footprints[compared_footprint]['end'] and compared_footprint in peak_footprints_new.keys():
-				#update the end position
-				peak_footprints_new[compared_footprint]['end'] = end_to_check
-				#update the length
-				peak_footprints_new[compared_footprint]['len'] = end_to_check - peak_footprints[compared_footprint]['end']
-				#update the score
-				peak_footprints_new[compared_footprint]['score'] = (peak_footprints[footprint_to_check]['score'] + peak_footprints[compared_footprint]['score']) / 2
+		if merge_footprints_left: #the left merging is enabled, start and end of compared_footprint should be smaller than the start of the footprint_to_check
+			print("entered left merging")
+			print(start_to_check, end_to_check)
+			print(peak_footprints[compared_footprint]['start'], peak_footprints[compared_footprint]['end'])
+			if start_to_check < peak_footprints[compared_footprint]['start']:
+				if footprint_to_check not in peak_footprints_new.keys():
+					print("left, footprint to check ", footprint_to_check, " not in peak_footprints_new")
+					#UPDATE
+					if any(footprint_to_check in merged_footprints[x] for x in merged_footprints.keys()): #true if footprint_to_check was already merged with someone
+						#print("footprint_to_check ", footprint_to_check, " was a part of some merging")
+						for k, v in merged_footprints.items():
+							if footprint_to_check in v:
+								main_footprint = k
+						print("make merging using the information from the merged_footprints and peak_footprints_new")
+						#UPDATE
+					else:
+						print("make normal update, using data from peak_footprints")
+						merged_footprints[footprint_to_check] = merged_footprints.get(footprint_to_check, [])
+						merged_footprints[footprint_to_check] = [compared_footprint]
+						print(merged_footprints)
+
+						print("saving ", footprint_to_check)
+						peak_footprints_new[footprint_to_check] = peak_footprints.get(footprint_to_check, {})
+						peak_footprints_new[footprint_to_check] = peak_footprints[footprint_to_check] #<-- update
+						#UPDATE
+
+				else: #the footprint_to_check is in peak_footprints_new already
+					if footprint_to_check in merged_footprints.keys():
+						print("footprint_to_check ", footprint_to_check, " was as main for merging already")
+						#UPDATE
+					elif any(footprint_to_check in merged_footprints[x] for x in merged_footprints.keys()):
+						print("footprint_to_check ", footprint_to_check, " was a part of some merging")
+						for k, v in merged_footprints.items():
+							if footprint_to_check in v:
+								main_footprint = k
+						#UPDATE
+					else:
+						print("merge now and add footprint_to_check to the merged_footprints")
+						merged_footprints[footprint_to_check] = merged_footprints.get(footprint_to_check, [])
+						merged_footprints[footprint_to_check] = [compared_footprint]
+						#UPDATE
+
+		elif merge_footprints_left == False: #the right merging is enabled, start and end of compared footprint should be bigger than the start of the footprint_to_check
+			print("entered right merging")
+			print(start_to_check, end_to_check)
+			print(peak_footprints[compared_footprint]['start'], peak_footprints[compared_footprint]['end'])
+			if end_to_check > peak_footprints[compared_footprint]['end']:
+				if compared_footprint not in peak_footprints_new.keys():
+					print("right, compared_footprint ", compared_footprint, " not in peak_footprints_new")					
+					if any(compared_footprint in merged_footprints[x] for x in merged_footprints.keys()):
+						print("compared_footprint ", compared_footprint, " was a part of some merging")
+						for k, v in merged_footprints.items():
+							if compared_footprint in v:
+								main_footprint = k
+						print("make merging using the information from the merged_footprints and peak_footprints_new")
+						#UPDATE
+					else:
+						print("make normal update, using data from peak footprints")
+						merged_footprints[compared_footprint] = merged_footprints.get(compared_footprint, [])
+						merged_footprints[compared_footprint] = [footprint_to_check]
+						print(merged_footprints)
+
+						print("saving ", compared_footprint)
+						peak_footprints_new[compared_footprint] = peak_footprints.get(compared_footprint, {})
+						peak_footprints_new[compared_footprint] = peak_footprints[compared_footprint]
+						#UPDATE
+				else:
+					if compared_footprint in merged_footprints.keys():
+						print("compared_footprint ", compared_footprint, " was as main for merging already")
+						#UPDATE
+					elif any(compared_footprint in merged_footprints[x] for x in merged_footprints.keys()):
+						#print("compared_footprint ", compared_footprint, " was a part of some merging")
+						for k, v in merged_footprints.items():
+							if compared_footprint in v:
+								main_footprint = k
+						#UPDATE
+					else:
+						print("merge now and add compared_footprint to the merged_footprints")
+						merged_footprints[compared_footprint] = merged_footprints.get(compared_footprint, [])
+						merged_footprints[compared_footprint] = [compared_footprint]
+						print(merged_footprints)
+						#UPDATE
+
 
 		else: #save the current footprint, as it should not be merged
 			peak_footprints_new[footprint_to_check] = peak_footprints_new.get(footprint_to_check, [])
 			peak_footprints_new[footprint_to_check] = peak_footprints[footprint_to_check]
 
+	print(len(peak_footprints_new))
+	for footprint in peak_footprints_new:
+		print(footprint)
+	sys.exit()
 	return peak_footprints_new
 
 #this function uses the information provided from the .bed file to look for footprints within the peaks of interest