def test_write_to_barcode_meta_csv():
bam_file = utils.get_test_data('10x-example/possorted_genome_bam.bam')
with utils.TempDirectory() as location:
single_barcode_fastas = tenx.bam_to_temp_fasta(
barcodes=None,
barcode_renamer=None,
delimiter="X",
bam_file=bam_file,
temp_folder=location)
single_barcode_fastas = "," .join(
itertools.chain(single_barcode_fastas))
all_fastas_sorted = tenx.get_fastas_per_unique_barcodes(
single_barcode_fastas)
tenx.barcode_umi_seq_to_fasta(
location,
"X",
True,
0,
location,
all_fastas_sorted)
csv = os.path.join(location, "meta.csv")
tenx.write_to_barcode_meta_csv(location, csv)
umi_counts = [6, 2, 6, 4, 15, 5, 2, 2]
read_counts = [312, 36, 251, 194, 594, 153, 2, 68]
for index, row in pd.read_csv(csv).iterrows():
assert umi_counts[index] == row[tenx.UMI_COUNT]
assert read_counts[index] == row[tenx.READ_COUNT]
def test_barcode_umi_seq_to_fasta():
bam_file = utils.get_test_data('10x-example/possorted_genome_bam.bam')
with utils.TempDirectory() as location:
single_barcode_fastas = tenx.bam_to_temp_fasta(
barcodes=None,
barcode_renamer=None,
delimiter="X",
bam_file=bam_file,
temp_folder=location)
single_barcode_fastas = "," .join(
itertools.chain(single_barcode_fastas))
all_fastas_sorted = tenx.get_fastas_per_unique_barcodes(
single_barcode_fastas)
tenx.barcode_umi_seq_to_fasta(
location,
"X",
True,
10,
location,
all_fastas_sorted)
fastas = glob.glob(
os.path.join(location, "*_bam2fasta.fasta"))
assert len(fastas) == 1
meta_txts = glob.glob(
os.path.join(location, "*_meta.txt"))
assert len(meta_txts) == 8
def test_filtered_bam_to_umi_fasta():
bam_file = utils.get_test_data(
'10x-example/possorted_genome_bam_filtered.bam')
fastas = tenx.bam_to_temp_fasta(barcodes=None,
barcode_renamer=None,
delimiter='X',
bam_file=bam_file)
assert len(list(fastas)) == 32
def test_bam_to_temp_fasta():
filename = utils.get_test_data('10x-example/barcodes.tsv')
bam_file = utils.get_test_data('10x-example/possorted_genome_bam.bam')
barcodes = tenx.read_barcodes_file(filename)
fastas = tenx.bam_to_temp_fasta(barcodes=barcodes,
barcode_renamer=None,
delimiter="X",
bam_file=bam_file)
assert len(list(fastas)) == 8
def test_get_fastas_per_unique_barcodes():
filename = utils.get_test_data('10x-example/barcodes.tsv')
renamer_filename = utils.get_test_data('10x-example/barcodes_renamer.tsv')
bam_file = utils.get_test_data('10x-example/possorted_genome_bam.bam')
barcodes = tenx.read_barcodes_file(filename)
with utils.TempDirectory() as location:
all_fastas = tenx.bam_to_temp_fasta(
barcodes=barcodes,
barcode_renamer=renamer_filename,
delimiter="X",
bam_file=bam_file,
temp_folder=location)
all_fastas = ",".join(itertools.chain(all_fastas))
fastas_sorted = tenx.get_fastas_per_unique_barcodes(all_fastas)
assert len(fastas_sorted) == 8