def test_run_bam2fasta_percell_no_shard():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data(
'10x-example/possorted_genome_bam.fastq.gz')
fasta_files = cli.percell(
['--filename', testdata1, '--save-fastas', location])
print(fasta_files)
barcodes = [filename.replace(".fasta", "") for filename in fasta_files]
assert len(barcodes) == 8
def test_run_bam2fasta_fq_percell_no_shard_nonzero_umi():
with utils.TempDirectory() as location:
testdata1 = utils.get_test_data(
'10x-example/possorted_genome_bam.fastq.gz')
fasta_files = cli.percell([
'--filename', testdata1, '--save-fastas', location,
'--min-umi-per-barcode', '10'
])
print(fasta_files)
barcodes = [filename.replace(".fastq", "") for filename in fasta_files]
assert len(barcodes) == 1
sequences_fastq = []
with screed.open(fasta_files[0]) as f:
for record in f:
sequences_fastq.append(record.sequence)
gt_data = utils.get_test_data(
'10x-example/groundtruth_fasta_sequences.txt')
with open(gt_data, "r") as f:
for index, line in enumerate(f.readlines()):
assert line.strip() in sequences_fastq, \
"failed at index {}".format(index)