def test(self, infile):
_f = anyfile(infile)
ff = rec_handler(_f)
gd = []
err_cnt = 0
for rec in ff:
if not rec.startswith('rs'):
continue
lines = rec.strip().split('\n')
self._parse_rsline(lines)
d = self._parse_GMAF(lines)
if not d:
err_cnt += 1
gd.append(d)
print(err_cnt)
return gd
def parse(self, infile):
print(os.path.split(infile)[1])
cnt = 0
err_d = {}
_f = anyfile(infile)
ff = rec_handler(_f)
for rec in ff:
if not rec.startswith('rs'):
continue
doc = self.parse_one_record(rec)
if isinstance(doc, dict):
cnt += 1
yield doc
else:
if doc in err_d:
err_d[doc] += 1
else:
err_d[doc] = 1
print(cnt, err_d)