/usr/lib/python3/dist-packages/vcf/cparse.pyx is in python3-pyvcf 0.6.7-2build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 | from model import _Call
cdef _map(func, iterable, bad='.'):
'''``map``, but make bad values None.'''
return [func(x) if x != bad else None
for x in iterable]
INTEGER = 'Integer'
FLOAT = 'Float'
NUMERIC = 'Numeric'
def parse_samples(
list names, list samples, samp_fmt,
list samp_fmt_types, list samp_fmt_nums, site):
cdef char *name, *fmt, *entry_type, *sample
cdef int i, j
cdef list samp_data = []
cdef dict sampdict
cdef list sampvals
n_samples = len(samples)
n_formats = len(samp_fmt._fields)
for i in range(n_samples):
name = names[i]
sample = samples[i]
# parse the data for this sample
sampdat = [None] * n_formats
sampvals = sample.split(':')
for j in range(n_formats):
if j >= len(sampvals):
break
vals = sampvals[j]
# short circuit the most common
if vals == '.' or vals == './.':
sampdat[j] = None
continue
entry_type = samp_fmt_types[j]
# TODO: entry_num is None for unbounded lists
entry_num = samp_fmt_nums[j]
# we don't need to split single entries
if entry_num == 1 or ',' not in vals:
if entry_type == INTEGER:
try:
sampdat[j] = int(vals)
except ValueError:
sampdat[j] = float(vals)
elif entry_type == FLOAT or entry_type == NUMERIC:
sampdat[j] = float(vals)
else:
sampdat[j] = vals
if entry_num != 1:
sampdat[j] = (sampdat[j])
continue
vals = vals.split(',')
if entry_type == INTEGER:
try:
sampdat[j] = _map(int, vals)
except ValueError:
sampdat[j] = map(float, vals)
elif entry_type == FLOAT or entry_type == NUMERIC:
sampdat[j] = _map(float, vals)
else:
sampdat[j] = vals
# create a call object
call = _Call(site, name, samp_fmt(*sampdat))
samp_data.append(call)
return samp_data
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