diff --git a/bin/1.1_footprint_extraction/footprints_extraction.py b/bin/1.1_footprint_extraction/footprints_extraction.py index fae040e..d1b0f8f 100644 --- a/bin/1.1_footprint_extraction/footprints_extraction.py +++ b/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)))