def test_run_toBig_rdthr_2_2():
''' '''
# Variables
args = {
'file': [
'tests/files/input_toBig_1.rck.gz',
'tests/files/input_toBig_2.rck.gz',
'tests/files/input_toBig_3.rck.gz'
],
'outputfile':
'tests/files/main_test.out',
'fithr':
'2',
'rdthr':
'2',
'ncores':
'2',
'abthr':
None,
'regionfile':
'tests/files/input_toBig.regions',
'chromfile':
'tests/files/input_toBig.chrom.size'
}
# Run
main_toBig(args)
# Expected
snv_expect = [11001, 11002, 11007, 11010, 11013, 11023]
ins_expect = [11005, 11022]
del_expect = [11017, 11030]
# Tests
bit = bitarray.bitarray(11030 + 1)
big_dict = load_big('tests/files/main_test.out')
# Check snv
bit.setall(False)
for i in snv_expect:
bit[i] = True
#end for
assert big_dict['13_snv'][:11031] == bit
# Check ins
bit.setall(False)
for i in ins_expect:
bit[i] = True
#end for
assert big_dict['13_ins'][:11031] == bit
# Check del
bit.setall(False)
for i in del_expect:
bit[i] = True
#end for
assert big_dict['13_del'][:11031] == bit
# Clean
os.remove('tests/files/main_test.out')
def test_run_toBig_rdthr_2_all_miss_pos():
''' '''
# Variables
args = {
'file': [
'tests/files/input_toBig_1.rck.gz',
'tests/files/input_toBig_2.rck.gz',
'tests/files/input_toBig_3.rck.gz',
'tests/files/input_toBig_miss_pos.rck.gz'
],
'outputfile':
'tests/files/main_test.out',
'fithr':
'4',
'rdthr':
'2',
'ncores':
'2',
'abthr':
None,
'regionfile':
'tests/files/input_toBig.regions',
'chromfile':
'tests/files/input_toBig.chrom.size'
}
# Run and Tests
with pytest.raises(Exception) as e:
assert main_toBig(args)
assert str(
e.value
) == '\nERROR in file: position 13:11006 in file tests/files/input_toBig_miss_pos.rck.gz is not consistent with other files\n'