Merge pull request #41 from loosolab/peak_calling

Peak calling to dev after resolving overlaps

bin/1.1_footprint_extraction/footprints_extraction.py

@@ -43,6 +43,7 @@ def parse_args():
 	parser.add_argument('--window_length', default=200, type=int, help='Please enter the length for a window, by defauld 200 bp.')
 	parser.add_argument('--step', default=100, type=int, help='Please enter a step to move the window, by default 100 bp.')
 	parser.add_argument('--percentage',  default=0, type=int, help='Please enter a percentage to be added to background while searching for footprints, by default 0%%.')
+	parser.add_argument('--max_bp_between', default=6, type=int, help='Please enter the number of bp allowed to be in between two footprints, by default 6 bp.')
 	parser.add_argument('--silent', action='store_true', help='While working with data write the information only into ./footprints_extraction.log.')
 	args = parser.parse_args()
 
@@ -154,6 +155,7 @@ def save_footprint(footprint_count, footprint_scores, peak_footprints, chromosom
 				old_start = peak_footprints[existing_footprint_name]['start']
 				old_end = peak_footprints[existing_footprint_name]['end']
 				old_score = peak_footprints[existing_footprint_name]['score']
+				old_length = peak_footprints[existing_footprint_name]['len']
 
 				if footprint_start >= old_start and footprint_start <= old_end: #the start of the new footprint is between the start and end of an old footprint
 					if footprint_end > old_end: #the new footprint is not completely inside the old one
@@ -163,19 +165,21 @@ def save_footprint(footprint_count, footprint_scores, peak_footprints, chromosom
 
 						peak_footprints[existing_footprint_name]['end'] = footprint_end
 						peak_footprints[existing_footprint_name]['score'] = footprint_score
+						peak_footprints[existing_footprint_name]['len'] = footprint_end - old_start
 						#we can not update the max_pos as we do not have the information about scores array of the existing footprint
 					#else: the new footprint is completely inside the old one, do nothing
 					save_current_footprint = False
 					break
 
 				elif footprint_end >= old_start and footprint_end <= old_end: #the end of the new footprint is between the start and end of an old footprint
-					if footprint_start < old_start: #the new footprint is not completely inside the old one
+					if footprint_start < old_start: #the new footprint is not completely inside the old one						
 						#update the information about the existing footprint
 						#find the average of both scores
 						footprint_score = (peak_footprints[existing_footprint_name]['score'] + footprint_score) / 2
 
 						peak_footprints[existing_footprint_name]['start'] = footprint_start
 						peak_footprints[existing_footprint_name]['score'] = footprint_score
+						peak_footprints[existing_footprint_name]['len'] = old_end - footprint_start
 					#else do nothing
 					save_current_footprint = False
 					break
@@ -191,7 +195,7 @@ def save_footprint(footprint_count, footprint_scores, peak_footprints, chromosom
 
 		if save_current_footprint == True:
 			#make sure to save this footprint			
-			footprint_name = "footprint_" + str(footprint_count)
+			footprint_name = "f_" + str(footprint_count)
 
 			peak_footprints[footprint_name] = peak_footprints.get(footprint_name, {})
 			peak_footprints[footprint_name] = {'chromosom': chromosom, 'start': footprint_start, 'end': footprint_end, 'score': footprint_score, 'len': len(footprint_scores), 'bonus': bonus_info_from_bed, 'max_pos': max_pos}
@@ -270,11 +274,62 @@ def search_in_window(peak_footprints, footprint_count, chromosom, peak_start, pe
 
 	return peak_footprints, footprint_count
 
+#this function checks if there are footprints with a small amount of bp in between, and if so, merges them together
+#if at this point there are still overlaps of footprints, this function will delete them
+#the input parameter are: dictionary with footprints within one peak, and the max number of bp allowed to be in between the footprints
+#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 = {}
+
+	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']
+
+		merge_footprints_left = None
+
+		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
+				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
+				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
+
+		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]
+
+	return peak_footprints_new
+
 #this function uses the information provided from the .bed file to look for footprints within the peaks of interest
 #as input the information from the original bed file, as well as bigwig file is needed
 #the optional parameters window_length, step and percentage are needed as well to use the sliding window algorithm and work with the "background" score
 #the output of this function is a dictionary contains all the found footprints ready to write to the output file
-def find_peaks_from_bw(bed_dictionary, bw_file, window_length, step, percentage):
+def find_peaks_from_bw(bed_dictionary, bw_file, window_length, step, percentage, max_bp_between):
 
 	logger.info('Looking for footprints within peaks...')
 
@@ -295,9 +350,11 @@ def find_peaks_from_bw(bed_dictionary, bw_file, window_length, step, percentage)
 			peak_end = int(positions[1])
 
 			scores_in_peak = np.nan_to_num(np.array(list(bw_open.values(chromosom, peak_start, peak_end)))) #save the scores to an array
-
 			peak_footprints, footprint_count = search_in_window(peak_footprints, footprint_count, chromosom, peak_start, peak_end, scores_in_peak, window_length, bed_dictionary[header], step, percentage)
 
+			#double check for overlaps and possibly merging of footprints having up to 5 bp in between
+			peak_footprints = check_and_merge(peak_footprints, max_bp_between)
+
 			for footprint_name in peak_footprints.keys():
 				all_footprints[footprint_name] = all_footprints.get(footprint_name, {})
 				all_footprints[footprint_name] = peak_footprints[footprint_name]
@@ -381,7 +438,7 @@ def main():
 	logger.info("The script footprints_extraction.py was called using these parameters: " + str(vars(args)))
 
 	bed_dictionary = make_bed_dictionary(args.bed)
-	all_footprints = find_peaks_from_bw(bed_dictionary, args.bigwig, args.window_length, args.step, args.percentage)
+	all_footprints = find_peaks_from_bw(bed_dictionary, args.bigwig, args.window_length, args.step, args.percentage, args.max_bp_between)
 	write_to_bed_file(all_footprints, args.output_file)
 
 	logger.info("the number of peaks: " + str(len(bed_dictionary)))