def test_csv_parser(self):
# standad file
fhand = open(join(TEST_DATA_DIR, 'csv', 'standard_ex.tsv'), 'rb')
var_info = {b'solcap_snp_sl_15058': {'chrom': b'chrom1', 'pos': 345},
b'solcap_snp_sl_60635': {'chrom': b'chrom1', 'pos': 346},
b'solcap_snp_sl_60604': {'chrom': b'chrom1', 'pos': 347}}
parser = CSVParser(fhand, var_info, first_sample_column=1,
sep=b'\t')
expected = [(b'chrom1', 345, b'solcap_snp_sl_15058', b'A',
[b'C', b'G'], None, None, None, [(b'GT', [(0, 0), (0, 0),
(0, 0), (0, 1),
(2, 2)])]),
(b'chrom1', 346, b'solcap_snp_sl_60635', b'G', None, None,
None, None, [(b'GT', [(0, 0), (0, 0), (0, 0), (0, 0),
(-1, -1)])]),
(b'chrom1', 347, b'solcap_snp_sl_60604', b'C', [b'T'],
None, None, None, [(b'GT', [(0, 0), (-1, -1), (1, 0),
(0, 0), (0, 0)])])]
assert list(parser.variations) == expected
fhand.close()
assert parser.samples == [b'SR-9', b'SR-12', b'SR-13', b'SR-15',
b'SR-18']
assert parser.max_field_lens['alt'] == 2
assert parser.ploidy == 2
# IUPAC file
fhand = open(join(TEST_DATA_DIR, 'csv', 'iupac_ex3.txt'), 'rb')
var_info = {b'1': {'chrom': b'SL2.40ch02', 'pos': 331954},
b'2': {'chrom': b'SL2.40ch02', 'pos': 681961},
b'3': {'chrom': b'SL2.40ch02', 'pos': 1511764}}
parser = CSVParser(fhand, var_info, first_sample_column=3,
first_gt_column=3, sep=b'\t',
gt_splitter=create_iupac_allele_splitter())
expected = [(b'SL2.40ch02', 331954, b'1', b'T', [b'G'], None, None,
None, [(b'GT', [(1, 1), (0, 0), (-1, -1)])]),
(b'SL2.40ch02', 681961, b'2', b'C', None, None, None,
None, [(b'GT', [(0, 0), (0, 0), (-1, -1)])]),
(b'SL2.40ch02', 1511764, b'3', b'A', [b'T'], None, None,
None, [(b'GT', [(1, 1), (1, 1), (0, 1)])]),
(b'SL2.40ch02', 331954, b'1', b'T', [b'G'], None, None,
None, [(b'GT', [(1, 1), (0, 0), (-1, -1)])])]
for var, expect in zip(parser.variations, expected):
assert var == expect
fhand.close()
assert parser.samples == [b'TS-1', b'TS-11', b'TS-21']
assert parser.max_field_lens['alt'] == 1
assert parser.ploidy == 2
# pandas csv
fhand = open(join(TEST_DATA_DIR, 'csv', 'pandas.csv'), 'rb')
var_info = {b'solcap_snp_sl_15058': {'chrom': b'chrom1', 'pos': 345},
b'solcap_snp_sl_60635': {'chrom': b'chrom1', 'pos': 346},
b'solcap_snp_sl_60604': {'chrom': b'chrom1', 'pos': 347}}
parser = CSVParser(fhand, var_info, first_sample_column=0, sep=b'\t')
expected = [(b'chrom1', 345, b'solcap_snp_sl_15058', b'A',
[b'C', b'G'], None, None, None, [(b'GT', [(0, 0), (0, 0),
(0, 0), (0, 1),
(2, 2)])]),
(b'chrom1', 346, b'solcap_snp_sl_60635', b'G', None, None,
None, None, [(b'GT', [(0, 0), (0, 0), (0, 0), (0, 0),
(-1, -1)])]),
(b'chrom1', 347, b'solcap_snp_sl_60604', b'C', [b'T'],
None, None, None, [(b'GT', [(0, 0), (-1, -1), (1, 0),
(0, 0), (0, 0)])])]
for var, expect in zip(parser.variations, expected):
assert var == expect
fhand.close()
assert parser.samples == [b'SR-9', b'SR-12', b'SR-13', b'SR-15',
b'SR-18']
assert parser.max_field_lens['alt'] == 2
assert parser.ploidy == 2
def test_create_iupac_splitter(self):
spliter = create_iupac_allele_splitter()
assert spliter(b'A') == (ord('A'), ord('A'))
assert spliter(b'-') == None
assert spliter(b'') == None
def test_put_vars_from_csv(self):
fhand_ex = open(join(TEST_DATA_DIR, 'csv', 'iupac_ex3.txt'), 'rb')
var_info = {b'1': {'chrom': b'SL2.40ch02', 'pos': 331954},
b'2': {'chrom': b'SL2.40ch02', 'pos': 681961},
b'3': {'chrom': b'SL2.40ch02', 'pos': 1511764}}
parser = CSVParser(fhand_ex, var_info, first_sample_column=3,
first_gt_column=3, sep=b'\t',
gt_splitter=create_iupac_allele_splitter(),
max_field_lens={'alt': 1},
max_field_str_lens={'alt': 1, 'chrom': 20,
'ref': 1})
with NamedTemporaryFile(suffix='.h5') as fhand:
os.remove(fhand.name)
h5 = VariationsH5(fhand.name, mode='w', ignore_overflows=True,
ignore_undefined_fields=True)
h5.put_vars(parser)
exp = [b'SL2.40ch02', b'SL2.40ch02', b'SL2.40ch02']
assert list(h5['/variations/chrom'][:]) == exp
alleles = list(zip(h5['/variations/ref'],
[alts[0] for alts in h5['/variations/alt']]))
exp = [(b'G', b'T'), (b'C', b''), (b'A', b'T')]
for als, aexp in zip(alleles, exp):
assert set(als) == set(aexp)
assert list(h5['/variations/pos'][:]) == [331954, 681961,
1511764]
exp1 = numpy.array([[[1, 1], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [1, 0]]])
exp2 = numpy.array([[[0, 0], [1, 1], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[1, 1], [1, 1], [0, 1]]])
for gts, exp_gts1, exp_gts2 in zip(h5['/calls/GT'][:], exp1, exp2):
for gt, ex1, ex2 in zip(gts, exp_gts1, exp_gts2):
assert set(gt) == set(ex1) or set(gt) == set(ex2)
if os.path.exists(fhand.name):
os.remove(fhand.name)
fhand_ex.close()
fhand_ex = open(join(TEST_DATA_DIR, 'csv',
'two_letter_coding_ex3.txt'), 'rb')
var_info = {b'1': {'chrom': b'SL2.40ch02', 'pos': 331954},
b'2': {'chrom': b'SL2.40ch02', 'pos': 681961},
b'3': {'chrom': b'SL2.40ch02', 'pos': 1511764}}
parser = CSVParser(fhand_ex, var_info, first_sample_column=3,
first_gt_column=3, sep=b'\t',
max_field_lens={'alt': 1},
max_field_str_lens={'alt': 1, 'chrom': 20,
'ref': 1})
h5 = VariationsArrays(ignore_overflows=True,
ignore_undefined_fields=True)
h5.put_vars(parser)
exp = [b'SL2.40ch02', b'SL2.40ch02', b'SL2.40ch02']
assert list(h5['/variations/chrom'][:]) == exp
alleles = list(zip(h5['/variations/ref'],
[alts[0] for alts in h5['/variations/alt']]))
exp = [(b'G', b'T'), (b'C', b''), (b'A', b'T')]
for als, aexp in zip(alleles, exp):
assert set(als) == set(aexp)
assert list(h5['/variations/pos'][:]) == [331954, 681961,
1511764]
exp1 = numpy.array([[[1, 1], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [1, 0]]])
exp2 = numpy.array([[[0, 0], [1, 1], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[1, 1], [1, 1], [0, 1]]])
for gts, exp_gts1, exp_gts2 in zip(h5['/calls/GT'][:], exp1, exp2):
for gt, ex1, ex2 in zip(gts, exp_gts1, exp_gts2):
assert set(gt) == set(ex1) or set(gt) == set(ex2)
fhand_ex.close()
def test_csv_parser(self):
# standad file
fhand = open(join(TEST_DATA_DIR, 'csv', 'standard_ex.tsv'), 'rb')
var_info = {b'solcap_snp_sl_15058': {'chrom': b'chrom1', 'pos': 345},
b'solcap_snp_sl_60635': {'chrom': b'chrom1', 'pos': 346},
b'solcap_snp_sl_60604': {'chrom': b'chrom1', 'pos': 347}}
parser = CSVParser(fhand, var_info, first_sample_column=1,
sep=b'\t')
expected = [(b'chrom1', 345, b'solcap_snp_sl_15058', b'A',
[b'C', b'G'], None, None, None, [(b'GT', [(0, 0), (0, 0),
(0, 0), (0, 1),
(2, 2)])]),
(b'chrom1', 346, b'solcap_snp_sl_60635', b'G', None, None,
None, None, [(b'GT', [(0, 0), (0, 0), (0, 0), (0, 0),
(-1, -1)])]),
(b'chrom1', 347, b'solcap_snp_sl_60604', b'C', [b'T'],
None, None, None, [(b'GT', [(0, 0), (-1, -1), (1, 0),
(0, 0), (0, 0)])])]
assert list(parser.variations) == expected
fhand.close()
assert parser.samples == [b'SR-9', b'SR-12', b'SR-13', b'SR-15',
b'SR-18']
assert parser.ploidy == 2
# IUPAC file
fhand = open(join(TEST_DATA_DIR, 'csv', 'iupac_ex3.txt'), 'rb')
var_info = {b'1': {'chrom': b'SL2.40ch02', 'pos': 331954},
b'2': {'chrom': b'SL2.40ch02', 'pos': 681961},
b'3': {'chrom': b'SL2.40ch02', 'pos': 1511764}}
parser = CSVParser(fhand, var_info, first_sample_column=3,
first_gt_column=3, sep=b'\t',
gt_splitter=create_iupac_allele_splitter())
expected = [(b'SL2.40ch02', 331954, b'1', b'T', [b'G'], None, None,
None, [(b'GT', [(1, 1), (0, 0), (-1, -1)])]),
(b'SL2.40ch02', 681961, b'2', b'C', None, None, None,
None, [(b'GT', [(0, 0), (0, 0), (-1, -1)])]),
(b'SL2.40ch02', 1511764, b'3', b'A', [b'T'], None, None,
None, [(b'GT', [(1, 1), (1, 1), (0, 1)])]),
(b'SL2.40ch02', 331954, b'1', b'T', [b'G'], None, None,
None, [(b'GT', [(1, 1), (0, 0), (-1, -1)])])]
for var, expect in zip(parser.variations, expected):
assert var == expect
fhand.close()
assert parser.samples == [b'TS-1', b'TS-11', b'TS-21']
assert parser.ploidy == 2
# pandas csv
fhand = open(join(TEST_DATA_DIR, 'csv', 'pandas.csv'), 'rb')
var_info = {b'solcap_snp_sl_15058': {'chrom': b'chrom1', 'pos': 345},
b'solcap_snp_sl_60635': {'chrom': b'chrom1', 'pos': 346},
b'solcap_snp_sl_60604': {'chrom': b'chrom1', 'pos': 347}}
parser = CSVParser(fhand, var_info, first_sample_column=0, sep=b'\t')
expected = [(b'chrom1', 345, b'solcap_snp_sl_15058', b'A',
[b'C', b'G'], None, None, None, [(b'GT', [(0, 0), (0, 0),
(0, 0), (0, 1),
(2, 2)])]),
(b'chrom1', 346, b'solcap_snp_sl_60635', b'G', None, None,
None, None, [(b'GT', [(0, 0), (0, 0), (0, 0), (0, 0),
(-1, -1)])]),
(b'chrom1', 347, b'solcap_snp_sl_60604', b'C', [b'T'],
None, None, None, [(b'GT', [(0, 0), (-1, -1), (1, 0),
(0, 0), (0, 0)])])]
for var, expect in zip(parser.variations, expected):
assert var == expect
fhand.close()
assert parser.samples == [b'SR-9', b'SR-12', b'SR-13', b'SR-15',
b'SR-18']
assert parser.ploidy == 2
def test_create_iupac_splitter(self):
spliter = create_iupac_allele_splitter()
assert spliter(b'A') == (ord('A'), ord('A'))
assert spliter(b'-') is None
assert spliter(b'') is None
def test_put_vars_from_csv(self):
fhand_ex = open(join(TEST_DATA_DIR, 'csv', 'iupac_ex3.txt'), 'rb')
var_info = {b'1': {'chrom': b'SL2.40ch02', 'pos': 331954},
b'2': {'chrom': b'SL2.40ch02', 'pos': 681961},
b'3': {'chrom': b'SL2.40ch02', 'pos': 1511764}}
parser = CSVParser(fhand_ex, var_info, first_sample_column=3,
first_gt_column=3, sep=b'\t',
gt_splitter=create_iupac_allele_splitter())
with NamedTemporaryFile(suffix='.h5') as fhand:
os.remove(fhand.name)
h5 = VariationsH5(fhand.name, mode='w',
ignore_undefined_fields=True)
h5.put_vars(parser)
exp = [b'SL2.40ch02', b'SL2.40ch02', b'SL2.40ch02']
assert list(h5['/variations/chrom'][:]) == exp
alleles = list(zip(h5['/variations/ref'],
[alts[0] for alts in h5['/variations/alt']]))
exp = [(b'G', b'T'), (b'C', b''), (b'A', b'T')]
for als, aexp in zip(alleles, exp):
assert set(als) == set(aexp)
assert list(h5['/variations/pos'][:]) == [331954, 681961,
1511764]
exp1 = numpy.array([[[1, 1], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [1, 0]]])
exp2 = numpy.array([[[0, 0], [1, 1], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[1, 1], [1, 1], [0, 1]]])
for gts, exp_gts1, exp_gts2 in zip(h5['/calls/GT'][:], exp1, exp2):
for gt, ex1, ex2 in zip(gts, exp_gts1, exp_gts2):
assert set(gt) == set(ex1) or set(gt) == set(ex2)
if os.path.exists(fhand.name):
os.remove(fhand.name)
fhand_ex.close()
fhand_ex = open(join(TEST_DATA_DIR, 'csv',
'two_letter_coding_ex3.txt'), 'rb')
var_info = {b'1': {'chrom': b'SL2.40ch02', 'pos': 331954},
b'2': {'chrom': b'SL2.40ch02', 'pos': 681961},
b'3': {'chrom': b'SL2.40ch02', 'pos': 1511764}}
parser = CSVParser(fhand_ex, var_info, first_sample_column=3,
first_gt_column=3, sep=b'\t')
h5 = VariationsArrays(ignore_undefined_fields=True)
h5.put_vars(parser)
exp = [b'SL2.40ch02', b'SL2.40ch02', b'SL2.40ch02']
assert list(h5['/variations/chrom'][:]) == exp
alleles = list(zip(h5['/variations/ref'],
[alts[0] for alts in h5['/variations/alt']]))
exp = [(b'G', b'T'), (b'C', b''), (b'A', b'T')]
for als, aexp in zip(alleles, exp):
assert set(als) == set(aexp)
assert list(h5['/variations/pos'][:]) == [331954, 681961,
1511764]
exp1 = numpy.array([[[1, 1], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[0, 0], [0, 0], [1, 0]]])
exp2 = numpy.array([[[0, 0], [1, 1], [-1, -1]],
[[0, 0], [0, 0], [-1, -1]],
[[1, 1], [1, 1], [0, 1]]])
for gts, exp_gts1, exp_gts2 in zip(h5['/calls/GT'][:], exp1, exp2):
for gt, ex1, ex2 in zip(gts, exp_gts1, exp_gts2):
assert set(gt) == set(ex1) or set(gt) == set(ex2)
fhand_ex.close()
