def calculate_mods_frequency(mods_files, prob_cf):
sitekeys = set()
sitekey2stats = dict()
count, used = 0, 0
for mods_file in mods_files:
if mods_file.endswith(".gz"):
infile = gzip.open(mods_file, 'rt')
else:
infile = open(mods_file, 'r')
for line in infile:
words = line.strip().split("\t")
mod_record = ModRecord(words)
if mod_record.is_record_callable(prob_cf):
if mod_record._site_key not in sitekeys:
sitekeys.add(mod_record._site_key)
sitekey2stats[mod_record._site_key] = SiteStats(mod_record._strand,
mod_record._pos_in_strand,
mod_record._kmer)
sitekey2stats[mod_record._site_key]._prob_0 += mod_record._prob_0
sitekey2stats[mod_record._site_key]._prob_1 += mod_record._prob_1
sitekey2stats[mod_record._site_key]._coverage += 1
if mod_record._called_label == 1:
sitekey2stats[mod_record._site_key]._met += 1
else:
sitekey2stats[mod_record._site_key]._unmet += 1
used += 1
count += 1
infile.close()
print("{:.2f}% ({} of {}) calls used..".format(used/float(count) * 100, used, count))
return sitekey2stats
def calculate_mods_frequency(mods_files, prob_cf):
sitekeys = set()
sitekey2stats = dict()
count, used = 0, 0
for mods_file in mods_files:
with open(mods_file, 'r') as rf:
for line in rf:
words = line.strip().split("\t")
mod_record = ModRecord(words)
if mod_record.is_record_callable(prob_cf):
if mod_record._site_key not in sitekeys:
sitekeys.add(mod_record._site_key)
sitekey2stats[mod_record._site_key] = SiteStats(mod_record._strand,
mod_record._pos_in_strand,
mod_record._kmer)
sitekey2stats[mod_record._site_key]._prob_0 += mod_record._prob_0
sitekey2stats[mod_record._site_key]._prob_1 += mod_record._prob_1
sitekey2stats[mod_record._site_key]._coverage += 1
if mod_record._called_label == 1:
sitekey2stats[mod_record._site_key]._met += 1
else:
sitekey2stats[mod_record._site_key]._unmet += 1
used += 1
count += 1
print("{} of {} samples used..".format(used, count))
return sitekey2stats
def sample_sites(filename, is_methylated):
all_crs = list()
rf = open(filename)
for line in rf:
mt_record = ModRecord(line.rstrip().split())
all_crs.append(
CallRecord(mt_record._site_key, mt_record._called_label,
is_methylated, mt_record._prob_0, mt_record._prob_1))
rf.close()
print('there are {} basemod candidates totally'.format(len(all_crs)))
random.shuffle(all_crs)
return all_crs