deleting the print statements, adding some comments

bin/1.1_footprint_extraction/footprints_extraction.py

@@ -285,8 +285,7 @@ def check_and_merge(peak_footprints, max_bp_between):
 	peak_footprints_new = {}
 	merged_footprints = {}
 
-	#print(len(peak_footprints))
-
+	#we need to check each footprint within this peak with the other footprints for possible merging
 	for footprint_to_check in peak_footprints.keys():
 		start_to_check = peak_footprints[footprint_to_check]['start']
 		end_to_check = peak_footprints[footprint_to_check]['end']
@@ -296,142 +295,93 @@ def check_and_merge(peak_footprints, max_bp_between):
 		for compared_footprint in peak_footprints.keys():
 
 			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)
+				#make compared_footprint longer: 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)
+				#make footprint_to_check longer: footprint_to_check + compared footprint
 				merge_footprints_left = True
 				break
 
 		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")
-					#even if it is not in keys, it could be merged already, so check first, if there are some footprints merged with this one
-					#print(merged_footprints)
 					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")
+						#make merging using the information from the merged_footprints and peak_footprints_new
 						#UPDATE
-						#print("update")
-						#print(peak_footprints_new[main_footprint])
 						peak_footprints_new[main_footprint] = footprint_update(peak_footprints_new[main_footprint], peak_footprints[compared_footprint]['start'], peak_footprints[main_footprint]['end'], peak_footprints[compared_footprint]['score'])
-						#print(peak_footprints_new[main_footprint])
 						merged_array = merged_footprints[main_footprint]
 						merged_array.append(compared_footprint)
 						merged_footprints[main_footprint] = merged_array
-						#print(merged_footprints)
 					#there are no merged footprints with the footprint_to_check yet, so make a new one
 					else:
-						#print("make normal update, using data from peak_footprints")
+						#add the compared footprint and 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]
-						#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
-						#print("update")
-						#print(peak_footprints_new[footprint_to_check])
 						peak_footprints_new[footprint_to_check] = footprint_update(peak_footprints_new[footprint_to_check], peak_footprints_new[footprint_to_check]['start'], peak_footprints[compared_footprint]['end'], peak_footprints[compared_footprint]['score'])
-						#print(peak_footprints_new[footprint_to_check])
 				else: #the footprint_to_check is in peak_footprints_new already
 					#the footprint_to_check can only be the main part of merging before, check it
 					if footprint_to_check in merged_footprints.keys():
-						#print("footprint_to_check ", footprint_to_check, " was as main for merging already")
+						#footprint_to_check was as main for merging already
 						#UPDATE
-						#print("update")
-						#print(peak_footprints_new[footprint_to_check])
 						peak_footprints_new[footprint_to_check] = footprint_update(peak_footprints_new[footprint_to_check], peak_footprints_new[footprint_to_check]['start'], peak_footprints[compared_footprint]['end'], peak_footprints[compared_footprint]['score'])
-						#print(peak_footprints_new[footprint_to_check])
-						#merged_footprints[footprint_to_check].append(compared_footprint)
+						#add it to the merged_footprints as well
 						merged_array = merged_footprints[footprint_to_check]
 						merged_array.append(compared_footprint)
 						merged_footprints[footprint_to_check] = merged_array
-						#print(merged_footprints)
-
 					else:
-						#print("merge now and add footprint_to_check to the merged_footprints")
+						#the footprint_to check was not merged with anything yet
 						merged_footprints[footprint_to_check] = merged_footprints.get(footprint_to_check, [])
 						merged_footprints[footprint_to_check] = [compared_footprint]
 						#UPDATE
-						#print("update")
-						#print(peak_footprints_new[footprint_to_check])
 						peak_footprints_new[footprint_to_check] = footprint_update(peak_footprints_new[footprint_to_check], peak_footprints_new[footprint_to_check]['start'], peak_footprints[compared_footprint]['end'], peak_footprints[compared_footprint]['score'])
-						#print(peak_footprints_new[footprint_to_check])
-		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'])
+		#the right merging is enabled, start and end of compared footprint should be bigger than the start of the footprint_to_check
+		elif merge_footprints_left == False: 
 			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 compared_footprint not in peak_footprints_new.keys():					
 					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")
+						#make merging using the information from the merged_footprints and peak_footprints_new
 						#UPDATE
-						#print("update")
-						#print(merged_footprints)
 						peak_footprints_new[main_footprint] = footprint_update(peak_footprints_new[main_footprint], peak_footprints[main_footprint]['start'], peak_footprints[footprint_to_check]['end'], peak_footprints[footprint_to_check]['score'])
-						#print(merged_footprints)
-						#merged_footprints[main_footprint] = merged_footprints[main_footprint].append(footprint_to_check)
+						#add to the merged_footprints
 						merged_array = merged_footprints[main_footprint]
 						merged_array.append(footprint_to_check)
 						merged_footprints[main_footprint] = merged_array
 					else:
-						#print("make normal update, using data from peak footprints")
+						#"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
-						#print("update")
-						#print(peak_footprints_new[compared_footprint])
 						peak_footprints_new[compared_footprint] = footprint_update(peak_footprints_new[compared_footprint], peak_footprints_new[compared_footprint]['start'], peak_footprints[footprint_to_check]['end'], peak_footprints[footprint_to_check]['score'])
-						#print(peak_footprints_new[compared_footprint])
 				else:
 					if compared_footprint in merged_footprints.keys():
-						#print("compared_footprint ", compared_footprint, " was as main for merging already")
+						#compared_footprint was as main for merging already
 						#UPDATE
-						#print("update")
-						#print(peak_footprints_new[compared_footprint])
 						peak_footprints_new[compared_footprint] = footprint_update(peak_footprints_new[compared_footprint], peak_footprints_new[compared_footprint]['start'], peak_footprints[footprint_to_check]['end'], peak_footprints[footprint_to_check]['score'])
-						#print(peak_footprints_new[compared_footprint])
-						#merged_footprints[compared_footprint] = merged_footprints[compared_footprint].append(footprint_to_check)
+
 						merged_array = merged_footprints[compared_footprint]
 						merged_array.append(footprint_to_check)
 						merged_footprints[compared_footprint] = merged_array
-						#print(merged_footprints)
+
 					else:
-						#print("merge now and add compared_footprint to the merged_footprints")
+						#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
-						#print("update")
-						#print(peak_footprints_new[compared_footprint])
 						peak_footprints_new[compared_footprint] = footprint_update(peak_footprints_new[compared_footprint], peak_footprints_new[compared_footprint]['start'], peak_footprints[footprint_to_check]['end'], peak_footprints[footprint_to_check]['score'])
-						#print(peak_footprints_new[compared_footprint])
 
 		else: #save the current footprint, as it should not be merged
 			peak_footprints_new[footprint_to_check] = peak_footprints_new.get(footprint_to_check, [])