def test_shard_bam_file():
filename = utils.get_test_data('10x-example/possorted_genome_bam.bam')
bam_file = tenx.read_bam_file(filename)
assert isinstance(bam_file, bs.AlignmentFile)
expected_alignments = sum(1 for _ in bam_file)
with utils.TempDirectory() as location:
bam_shard_files = tenx.shard_bam_file(filename, expected_alignments,
location)
assert len(bam_shard_files) == 1
num_shards = 2
with utils.TempDirectory() as location:
bam_shard_files = tenx.shard_bam_file(
filename, expected_alignments // num_shards, location)
assert len(bam_shard_files) == 2
total_alignments = 0
for bam_file in bam_shard_files:
total_alignments += sum(1 for _ in tenx.read_bam_file(bam_file))
assert total_alignments == expected_alignments
whole_bam_file = tenx.read_bam_file(filename)
for bam_file in bam_shard_files:
for line in tenx.read_bam_file(bam_file):
assert line == next(whole_bam_file)
def test_pass_alignment_qc_filtered():
bam = tenx.read_bam_file(
utils.get_test_data('10x-example/possorted_genome_bam_filtered.bam'))
total_alignments = sum(1 for _ in bam)
bam = tenx.read_bam_file(
utils.get_test_data('10x-example/possorted_genome_bam_filtered.bam'))
assert total_alignments == 1500
total_pass = sum(1 for alignment in bam
if tenx.pass_alignment_qc(alignment, None))
assert total_pass == 192
def test_pass_alignment_qc():
barcodes = tenx.read_barcodes_file(
utils.get_test_data('10x-example/barcodes.tsv'))
bam = tenx.read_bam_file(
utils.get_test_data('10x-example/possorted_genome_bam.bam'))
total_pass = sum(1 for alignment in bam
if tenx.pass_alignment_qc(alignment, barcodes))
assert total_pass == 439
def test_read_bam_file():
filename = utils.get_test_data('10x-example/possorted_genome_bam.bam')
bam_file = tenx.read_bam_file(filename)
assert isinstance(bam_file, bs.AlignmentFile)
total_alignments = sum(1 for _ in bam_file)
assert total_alignments == 1714