From b2f37731d5864d15145816a49a410a1aab0dd9af Mon Sep 17 00:00:00 2001 From: anastasiia Date: Thu, 10 Jan 2019 12:13:35 +0100 Subject: [PATCH] the max_pos is the index, and so add always 1 after calculating it. Otherwise it could be 0 as index --- bin/1.1_footprint_extraction/footprints_extraction.py | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/bin/1.1_footprint_extraction/footprints_extraction.py b/bin/1.1_footprint_extraction/footprints_extraction.py index ab294d2..f8fea5a 100644 --- a/bin/1.1_footprint_extraction/footprints_extraction.py +++ b/bin/1.1_footprint_extraction/footprints_extraction.py @@ -143,6 +143,8 @@ def save_footprint(footprint_count, footprint_scores, peak_footprints, chromosom else: max_pos = first_max_pos + max_pos = max_pos + 1 #as the index of an array starts with 0 + #calculate the score for the current footprint as mean of all scores from the bigwig file footprint_score = np.mean(footprint_scores) @@ -527,6 +529,10 @@ def write_to_bed_file(all_footprints, sorted_output_file_name): #write each footprint line for line to the output file for footprint in all_footprints: + #if footprint[1]['start'] >= footprint[1]['end']: + # print(footprint) + #if footprint[1]['max_pos'] == 0: + # print(footprint) output_file.write('\t'.join([footprint[1]['chromosom'], str(footprint[1]['start']), str(footprint[1]['end']), footprint[0], str(round(footprint[1]['score'], 6)), '.', str(footprint[1]['len']), str(footprint[1]['max_pos']), ';'.join(footprint[1]['bonus'])]) + '\n') output_file.close()