changing the name of max_bp_between to min_gap

bin/1.1_footprint_extraction/footprints_extraction.py

@@ -44,7 +44,7 @@ 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('--min_gap', 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()
 
@@ -281,7 +281,7 @@ def search_in_window(peak_footprints, footprint_count, chromosom, peak_start, pe
 #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):
+def check_and_merge(peak_footprints, min_gap):
 	#to ensure the merging works well, sort the footprints first arter start and end positions
 	#the sort can not be applied to a dictionary, we are making a list out of peak_footprints_dict
 	peak_footprints_list = sorted(peak_footprints.items(), key = lambda x : (x[1]['start'], x[1]['end']), reverse = False)
@@ -300,11 +300,11 @@ 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:
+			if start_to_check > peak_footprints[compared_footprint]['start'] and start_to_check - peak_footprints[compared_footprint]['end'] < min_gap:
 				#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:
+			elif end_to_check < peak_footprints[compared_footprint]['end'] and peak_footprints[compared_footprint]['start'] - end_to_check < min_gap:
 				#make footprint_to_check longer: footprint_to_check + compared footprint
 				merge_footprints_left = True
 				break
@@ -413,7 +413,7 @@ def footprint_update(footprint, start, end, score):
 #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, max_bp_between):
+def find_peaks_from_bw(bed_dictionary, bw_file, window_length, step, percentage, min_gap):
 
 	logger.info('Looking for footprints within peaks...')
 
@@ -437,7 +437,7 @@ def find_peaks_from_bw(bed_dictionary, bw_file, window_length, step, percentage,
 			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)
+			peak_footprints = check_and_merge(peak_footprints, min_gap)
 
 			for footprint_name in peak_footprints.keys():
 				all_footprints[footprint_name] = all_footprints.get(footprint_name, {})
@@ -533,7 +533,7 @@ 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, args.max_bp_between)
+	all_footprints = find_peaks_from_bw(bed_dictionary, args.bigwig, args.window_length, args.step, args.percentage, args.min_gap)
 	write_to_bed_file(all_footprints, args.output_file)
 
 	logger.info("the number of peaks: " + str(len(bed_dictionary)))