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Peak calling #15

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Dec 19, 2018
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Merged

Peak calling #15

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4ec60f7
Merge pull request #13 from loosolab/dev
renewiegandt Dec 19, 2018
b74af7f
changing the separator in the last line
anastasiia Dec 19, 2018
117ab50
adding a column name strand containing always .
anastasiia Dec 19, 2018
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4 changes: 2 additions & 2 deletions bin/footprints_extraction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -284,7 +284,7 @@ def find_peaks_from_bw(bed_dictionary, bw_file, window_length, step, percentage)
def write_to_bed_file(all_footprints, sorted_output_file_name):
output_file_name = "not_sorted_" + sorted_output_file_name #save in the working directory

header = ["#chr", "start", "end", "name", "score", "len", "max_pos", "bonus_info"] #a header to know what is in the columns
header = ["#chr", "start", "end", "name", "score", "strand", "len", "max_pos", "bonus_info"] #a header to know what is in the columns

output_file = open(output_file_name, 'w') #open a file to write

Expand All @@ -294,7 +294,7 @@ 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:
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']), '\t'.join(footprint[1]['bonus'])]) + '\n')
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()

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