def test_write_vcf_from_h5(self):
# With hdf5 file
tomato_h5 = VariationsH5(join(TEST_DATA_DIR,
'tomato.apeki_gbs.calmd.h5'), "r")
exp_fhand = open(join(TEST_DATA_DIR, "tomato.apeki_100_exp.vcf"), "rb")
with NamedTemporaryFile(mode='wb') as tmp_fhand:
write_vcf(tomato_h5, tmp_fhand)
# only checking snps
exp_lines = list(exp_fhand)
exp_lines = [line for line in exp_lines
if not line.startswith(b'#')]
with open(tmp_fhand.name, 'rb') as refhand:
i = 0
for line in refhand:
if line.startswith(b'#'):
continue
try:
assert line == exp_lines[i]
except AssertionError:
print(line.decode())
print(exp_lines[i].decode())
i += 1
if i > 42:
break
exp_fhand.close()
def test_generated_vcf_feed_outputs_equal_vcfs(self):
h5_vars = VariationsH5(
join(TEST_DATA_DIR, 'tomato.apeki_gbs.calmd.1stchunk.h5'), "r")
with NamedTemporaryFile(mode='wb') as vcf_vars_from_h5:
write_vcf(h5_vars, vcf_vars_from_h5)
vcf_vars_from_h5.flush()
vcf_fhand = open(vcf_vars_from_h5.name, 'rb')
vcf = VCFParser(vcf_fhand)
vcf_vars_parsed = VariationsArrays()
vcf_vars_parsed.put_vars(vcf)
with NamedTemporaryFile(mode='wb') as vcf_vars_from_vcf:
vcf_vars_parsed.write_vcf(vcf_vars_from_vcf)
vcf_vars_from_vcf.flush()
vcf_from_h5_fhand = open(vcf_vars_from_h5.name, 'rb')
vcf_from_vcf_fhand = open(vcf_vars_from_vcf.name, 'rb')
for line_parsed_from_h5, line_parsed_from_vcf in zip(
vcf_from_h5_fhand, vcf_from_vcf_fhand):
assert line_parsed_from_h5 == line_parsed_from_vcf, "when importing from a generated VCF and exporting to a new VCF both files must be the same"
def write_vcf(self, vcf_fhand):
write_vcf(self, vcf_fhand)
def write_vcf(self, vcf_fhand):
write_vcf(self, vcf_fhand)
def test_write_vcf(self):
# With all fields available
tmp_fhand = NamedTemporaryFile()
tmp_fhand.close()
vcf_fhand = open(join(TEST_DATA_DIR, 'format_def_exp.vcf'), 'rb')
vcf = VCFParser(vcf_fhand, max_field_lens={'alt': 2},
pre_read_max_size=10000)
max_field_lens = {'CALLS': {b'GT': 1, b'HQ': 2, b'DP': 1, b'GQ': 1},
'FILTER': 1,
'INFO': {b'AA': 1, b'AF': 2, b'DP': 1,
b'DB': 1, b'NS': 1, b'H2': 1}, 'alt': 2}
max_field_str_lens = {'INFO': {b'AA': 1}, 'alt': 5, 'chrom': 2, 'ref': 4,
'id': 10, 'FILTER': 0}
variations = VariationsArrays(ignore_undefined_fields=True)
variations.put_vars(vcf, max_field_lens=max_field_lens,
max_field_str_lens=max_field_str_lens)
vcf_fhand.close()
with NamedTemporaryFile(mode='wb') as out_fhand:
write_vcf(variations, out_fhand, vcf_format='VCFv4.0')
vcf_fpath = join(TEST_DATA_DIR, 'format_def_exp.vcf')
with open(vcf_fpath, 'r') as exp_fhand:
exp_lines = list(exp_fhand)
out_fhand.seek(0)
with open(out_fhand.name) as refhand:
for line in refhand:
try:
assert line in exp_lines
except AssertionError:
print('aa', line)
# With missing info in variations
tmp_fhand = NamedTemporaryFile()
out_fpath = tmp_fhand.name
tmp_fhand.close()
vcf_fhand = open(join(TEST_DATA_DIR, 'format_def_without_info.vcf'),
'rb')
vcf = VCFParser(vcf_fhand)
max_field_lens = {'INFO': {}, 'CALLS': {b'GQ': 1, b'GT': 1, b'HQ': 2,
b'DP': 1},
'FILTER': 1, 'alt': 2}
max_field_str_lens = {'ref': 4, 'INFO': {}, 'id': 10, 'FILTER': 0,
'alt': 5, 'chrom': 2}
h5_without_info = VariationsH5(fpath=out_fpath, mode='w',
ignore_undefined_fields=True)
h5_without_info.put_vars(vcf, max_field_lens=max_field_lens,
max_field_str_lens=max_field_str_lens)
vcf_fhand.close()
with NamedTemporaryFile(mode='wb') as out_fhand:
write_vcf(h5_without_info, out_fhand, vcf_format='VCFv4.0')
vcf_fpath = join(TEST_DATA_DIR, 'format_def_without_info_exp.vcf')
with open(vcf_fpath, 'r') as exp_fhand:
exp_lines = list(exp_fhand)
out_fhand.seek(0)
with open(out_fhand.name) as refhand:
for line in refhand:
try:
assert line in exp_lines
except AssertionError:
print(line)
