def test_read_write(tmp_path):
records = [
busio.Bus_record(0, 0, 10, 20, 1),
busio.Bus_record(1, 0, 13, 206, 12),
busio.Bus_record(2, 0, 14, 250, 13)
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=1, umi_length=2)
# check that file got created
assert pathlib.Path(fname).exists()
# check that read/write are inverses of each other
# buffersize is on purpose smaller then len(records)
new_records = list(
busio.read_binary_bus(fname, decode_seq=False, buffersize=2))
assert new_records == records
# buffersize larger
new_records = list(
busio.read_binary_bus(fname, decode_seq=False, buffersize=20))
assert new_records == records
# check the decode_Seq works:
record = next(busio.read_binary_bus(fname, decode_seq=False, buffersize=2))
assert isinstance(record.CB, int) and isinstance(record.UMI, int)
record = next(busio.read_binary_bus(fname, decode_seq=True, buffersize=2))
assert isinstance(record.CB, str) and isinstance(record.UMI, str)
def test_iterate_cells_UMI_raise_unsorted(tmp_path):
"""
iterate_CB_UMI_of_busfile must raise an error of the busfile is unsorted (in terms of CBs)
"""
records = [
busio.Bus_record('ATAT', 'TAT', 14, 250, 13),
busio.Bus_record('ATAT', 'AAA', 10, 20, 1),
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
with pytest.raises(ValueError):
gen = pybustools.iterate_CB_UMI_of_busfile(fname)
list(gen)
"""
also check that it raises when the CB is unsorted
"""
records = [ # impotant: the UMI should be the same,
busio.Bus_record('TTAT', 'TAT', 14, 250, 13),
busio.Bus_record('ATAT', 'TAT', 10, 20, 1),
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
with pytest.raises(ValueError):
gen = pybustools.iterate_CB_UMI_of_busfile(fname)
list(gen)
def test_iterate_cb_umi(tmp_path):
records = [
busio.Bus_record('ATAT', 'AAA', 10, 20, 1),
busio.Bus_record('ATAT', 'GGG', 10, 20, 1),
busio.Bus_record('ATAT', 'GGG', 11, 20, 1),
busio.Bus_record('TAGA', 'TAT', 14, 250, 13),
busio.Bus_record('TTAT', 'AAA', 13, 206, 12),
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
gen = pybustools.iterate_CB_UMI_of_busfile(fname)
# the first record must have one entry
cb1, list1 = next(gen)
assert cb1 == ('ATAT', 'AAA') and len(list1) == 1
cb2, list2 = next(gen)
assert cb2 == ('ATAT', 'GGG') and len(list2) == 2
cb3, list3 = next(gen)
assert cb3 == ('TAGA', 'TAT') and len(list3) == 1
cb4, list4 = next(gen)
assert cb4 == ('TTAT', 'AAA') and len(list4) == 1
def test_write_check_cb_umi_length(tmp_path):
"""
make sure an exception is thrown if the records dont match the given UMI/CB length
"""
records = [
busio.Bus_record('ATAT', 'GGG', 10, 20, 1),
busio.Bus_record('TTA', 'AAA', 13, 206, 12),
]
fname = tmp_path / 'some.bus'
with pytest.raises(AssertionError):
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
def test_get_header(tmp_path):
records = [
busio.Bus_record(0, 0, 10, 20, 1),
busio.Bus_record(1, 0, 13, 206, 12),
busio.Bus_record(2, 0, 14, 250, 13)
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=12, umi_length=5)
_, cb, umi, _ = busio.get_header_info(fname)
assert cb == 12 and umi == 5
def test_iterate_cells_raise_unsorted(tmp_path):
"""
iterate_cells must raise an error of the busfile is unsorted (in terms of CBs)
"""
records = [
busio.Bus_record('TTAT', 'AAA', 13, 206, 12),
busio.Bus_record('ATAT', 'AAA', 10, 20, 1),
busio.Bus_record('TAGA', 'TAT', 14, 250, 13),
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
with pytest.raises(ValueError):
gen = pybustools.iterate_cells_of_busfile(fname)
list(gen)
def test_read_write_str(tmp_path):
"""
write records with strings instead of ints for CB/UMI
"""
records = [
busio.Bus_record('ATAT', 'GGG', 10, 20, 1),
busio.Bus_record('TTAT', 'AAA', 13, 206, 12),
busio.Bus_record('TAGA', 'TAT', 14, 250, 13)
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
# read and compare to originl
new_records = list(
busio.read_binary_bus(fname, decode_seq=True, buffersize=2))
assert new_records == records
def test_emit_records(tmp_path, ec_matrix_file, transcript_file):
"""
two busfiles, they have the same CB/UMI, but it maps to different EC/genes
emit_records_based_on_gene should yield multiple entries!!
"""
cb_length = 4
umi_length = 3
records1 = [ # # CB UMI EC COUNT FLAG
busio.Bus_record('ATAT', 'GGG', 1, 10, 1),
]
fname1 = tmp_path / 'some1.bus'
busio.write_busfile(fname1, records1, cb_length, umi_length)
bus1 = Bus(folder='/',
bus_name=fname1,
ec_name=ec_matrix_file,
transcript_name=transcript_file)
records2 = [
busio.Bus_record('ATAT', 'GGG', 9, 20, 1),
]
fname2 = tmp_path / 'some2.bus'
busio.write_busfile(fname2, records2, cb_length, umi_length)
bus2 = Bus(folder='/',
bus_name=fname2,
ec_name=ec_matrix_file,
transcript_name=transcript_file)
busobject_dict = {'s1': bus1, 's2': bus2}
bus_iter = iterate_bus_cells_umi_multiple(['s1', 's2'], [fname1, fname2],
decode_seq=False)
for (cb_, umi_), info_dict_ in bus_iter:
# THIS SPLIts according to same gene
print('----------')
print(info_dict_)
print('----------')
counter = 0
for (cb, umi), info_dict in emit_records_based_on_gene(
cb_, umi_, info_dict_, busobject_dict):
counter += 1
print(cb, umi)
print(info_dict)
assert counter == 2
def test_subsampling(tmp_path):
# creating a total of 3 UMIs, nbut 10 counts
records = [
# CB UMI EC COUNT FLAG
busio.Bus_record(0, 0, 1, 3, 1),
busio.Bus_record(1, 0, 2, 3, 12),
busio.Bus_record(2, 0, 3, 4, 13)
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=1, umi_length=2)
fname_out = tmp_path / 'sub.bus'
subsampling.subsample_busfile(fname, fname_out, fraction=0.5)
# check the number of reads in the subsampled version
nreads, nmol = subsampling.get_number_of_reads_and_molecules(fname_out)
assert nreads == 5
def random_busrecord(cb_length, umi_length, ngenes):
d = {0: 'A', 1: 'C', 2: 'G', 3: 'T'}
cb = [random.randrange(0, 4) for _ in range(cb_length)]
cb = ''.join([d[_] for _ in cb])
umi = [random.randrange(0, 4) for _ in range(umi_length)]
umi = ''.join([d[_] for _ in umi])
gene = random.randrange(0, ngenes)
counts = random.randint(0, 50)
return busio.Bus_record(cb, umi, gene, counts, 1)
def test_return_busrecord(tmp_path):
"""
make sure the functions return the namedtuple, not just the tuple
"""
records = [
busio.Bus_record('ATAT', 'AAA', 10, 20, 1),
busio.Bus_record('ATAT', 'GGG', 10, 20, 1),
busio.Bus_record('TAGA', 'TAT', 14, 250, 13),
busio.Bus_record('TTAT', 'AAA', 13, 206, 12),
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
for cb, record_list in pybustools.iterate_cells_of_busfile(fname):
for r in record_list:
assert isinstance(r, busio.Bus_record)
for cbumi, record_list in pybustools.iterate_CB_UMI_of_busfile(fname):
for r in record_list:
assert isinstance(r, busio.Bus_record)
def test_fingerprint(tmp_path, ec_matrix_file, transcript_file):
"""
This should create 3 fingerprints:
[10, 0] x 2
[99, 0] x 1
[0, 20] x 1
"""
cb_length = 4
umi_length = 3
records1 = [ # # CB UMI EC COUNT FLAG
busio.Bus_record('ATAT', 'GGG', 1, 10, 1),
busio.Bus_record('ATAT', 'TTT', 1, 10, 1),
busio.Bus_record('CTAT', 'GGG', 1, 99, 1),
]
fname1 = tmp_path / 'some1.bus'
busio.write_busfile(fname1, records1, cb_length, umi_length)
bus1 = Bus(folder='/',
bus_name=fname1,
ec_name=ec_matrix_file,
transcript_name=transcript_file)
records2 = [
busio.Bus_record('ATAT', 'GGG', 9, 20, 1),
]
fname2 = tmp_path / 'some2.bus'
busio.write_busfile(fname2, records2, cb_length, umi_length)
bus2 = Bus(folder='/',
bus_name=fname2,
ec_name=ec_matrix_file,
transcript_name=transcript_file)
busobject_dict = {'s1': bus1, 's2': bus2}
df, _cond = phantom_create_dataframes(busobject_dict)
print(df)
assert len(df) == 3
assert df['freq'].sum() == 4
def test_iterate_cells(tmp_path):
records = [
busio.Bus_record('ATAT', 'AAA', 10, 20, 1),
busio.Bus_record('ATAT', 'GGG', 10, 20, 1),
busio.Bus_record('TAGA', 'TAT', 14, 250, 13),
busio.Bus_record('TTAT', 'AAA', 13, 206, 12),
]
fname = tmp_path / 'some.bus'
busio.write_busfile(fname, records, cb_length=4, umi_length=3)
gen = pybustools.iterate_cells_of_busfile(fname)
# the first record must have two uMIs
cb1, list1 = next(gen)
assert cb1 == 'ATAT' and len(list1) == 2
assert list1 == records[:2]
cb2, list2 = next(gen)
assert cb2 == 'TAGA' and len(list2) == 1
assert list2 == [records[2]]
cb3, list3 = next(gen)
assert cb3 == 'TTAT' and len(list3) == 1
assert list3 == [records[3]]