if unfiltered == 't':
print('Saving CoGe-formatted unfiltered file to:\n',
coge_unfiltered_path)
# Create an output for CoGe upload
if min_coverage:
coge_filtered_csv = open(coge_filtered_path, 'w')
coge_formatted_filtered = csv.writer(coge_filtered_csv)
if unfiltered == 't':
coge_unfiltered_csv = open(coge_unfiltered_path, 'w')
coge_formatted_unfiltered = csv.writer(coge_unfiltered_csv)
# Iterate over the dictionary for file-outputs
for chrm in bismark_data:
for pos in bismark_data[chrm]:
chrm_key = fix_chromosome_id(chrm)
pos_key = int(pos) - 1 # Subtract 1 from position to fix alignment with sequence in CoGe
dec_met = bismark_data[chrm][pos]['dec_met']
total = bismark_data[chrm][pos]['total']
strand = bismark_data[chrm][pos]['strand']
if min_coverage and total >= min_coverage:
coge_formatted_filtered.writerow(
[chrm_key, pos_key, pos_key, strand, dec_met, total]) # Output as filtered .csv file
if unfiltered == 't':
coge_formatted_unfiltered.writerow(
[chrm_key, pos_key, pos_key, strand, dec_met, total]) # Output as unfiltered .csv file
print('\nDone!')
methylKit_formatted = open(methyl_path, 'r')
methylation_summary = csv.reader(methylKit_formatted, delimiter='\t')
if min_coverage:
coge_filtered_csv = open(coge_filtered_path, 'w')
coge_formatted_filtered = csv.writer(coge_filtered_csv)
if unfiltered == 't':
coge_unfiltered_csv = open(coge_unfiltered_path, 'w')
coge_formatted_unfiltered = csv.writer(coge_unfiltered_csv)
# Write to output files depending on coverage filtered or not
next(methylation_summary) # Skip header
for row in methylation_summary:
chrm = fix_chromosome_id(row[1])
pos = int(row[2]) - 1
strand = row[3]
if strand == 'F':
strand = '1'
elif strand == 'R':
strand = '-1'
coverage = int(row[4])
dec_met = row[5]
if min_coverage and coverage >= min_coverage:
coge_formatted_filtered.writerow(
[chrm, pos, pos, strand, dec_met, coverage]) # Output as filtered .csv file
if unfiltered == 't':
coge_formatted_unfiltered.writerow(
[chrm, pos, pos, strand, dec_met, coverage]) # Output as unfiltered .csv file
