def write_sitekey2stats(sitekey2stats, result_file, is_sort, is_bed):
if is_sort:
keys = sorted(list(sitekey2stats.keys()), key=lambda x: split_key(x))
else:
keys = list(sitekey2stats.keys())
with open(result_file, 'w') as wf:
# wf.write('\t'.join(['chromosome', 'pos', 'strand', 'pos_in_strand', 'prob0', 'prob1',
# 'met', 'unmet', 'coverage', 'Rmet', 'kmer']) + '\n')
for key in keys:
chrom, pos = split_key(key)
sitestats = sitekey2stats[key]
assert(sitestats._coverage == (sitestats._met + sitestats._unmet))
if sitestats._coverage > 0:
rmet = float(sitestats._met) / sitestats._coverage
if is_bed:
wf.write("\t".join([chrom, str(pos), str(pos + 1), ".", str(sitestats._coverage),
sitestats._strand,
str(pos), str(pos + 1), "0,0,0", str(sitestats._coverage),
str(int(round(rmet * 100, 0)))]) + "\n")
else:
wf.write("%s\t%d\t%s\t%d\t%.3f\t%.3f\t%d\t%d\t%d\t%.4f\t%s\n" % (chrom, pos, sitestats._strand,
sitestats._pos_in_strand,
sitestats._prob_0,
sitestats._prob_1,
sitestats._met, sitestats._unmet,
sitestats._coverage, rmet,
sitestats._kmer))
else:
print("{} {} has no coverage..".format(chrom, pos))
def write_sitekey2stats(sitekey2stats, result_file):
sorted_keys = sorted(list(sitekey2stats.keys()),
key=lambda x: split_key(x))
with open(result_file, 'w') as wf:
# wf.write('\t'.join(['chromosome', 'pos', 'strand', 'pos_in_strand', 'prob0', 'prob1',
# 'met', 'unmet', 'coverage', 'Rmet', 'kmer']) + '\n')
for key in sorted_keys:
chrom, pos = split_key(key)
sitestats = sitekey2stats[key]
assert (sitestats._coverage == (sitestats._met + sitestats._unmet))
if sitestats._coverage > 0:
rmet = float(sitestats._met) / sitestats._coverage
wf.write("%s\t%d\t%s\t%d\t%.3f\t%.3f\t%d\t%d\t%d\t%.3f\t%s\n" %
(chrom, pos, sitestats._strand,
sitestats._pos_in_strand, sitestats._prob_0,
sitestats._prob_1, sitestats._met, sitestats._unmet,
sitestats._coverage, rmet, sitestats._kmer))
else:
print("{} {} has no coverage..".format(chrom, pos))