def main(outdir, r1, r2, barcodes, no_trim, overwrite, prefix, max_mismatches):
r"""
Demultiplex a paired-end fastq file into several based on unique barcodes.
The barcodes are sequences attached at the beginning of each read.
By default, it trimms the barcodes off the demultiplexed reads,
unless --no-trim is passed.
The barcodes text file should be formatted to have 1 column with
the barcodes, and an optional additional column to assign names to
the demultiplexed result files. the following structure:
\b
ATTCGT A1
ATATTC A2
TCGGAC B1
TCGAGG B2
"""
prefix = prefix if prefix.endswith('_') else f'{prefix}_'
commands.demultiplex(
barcodes_path=barcodes,
max_mismatches=max_mismatches,
no_trim=no_trim,
prefix=prefix,
output_dir=outdir,
overwrite=overwrite,
r1_path=r1,
r2_path=r2,
)
def test_prefix(tmpdir):
params = {
'barcodes_path': TEST_BARCODES,
'max_mismatches': 1,
'not_trim': True,
'output_dir': tmpdir.strpath,
'overwrite': True,
'prefix': 'my_weird_prefix',
'r1_path': TEST_R1,
'r2_path': TEST_R2,
}
commands.demultiplex(*params.values())
assert_output(**params)
def test_overwrite(tmpdir):
params = {
'barcodes_path': TEST_BARCODES,
'max_mismatches': 1,
'not_trim': False,
'output_dir': tmpdir.strpath,
'overwrite': True,
'prefix': '',
'r1_path': TEST_R1,
'r2_path': TEST_R2,
}
commands.demultiplex(*params.values())
commands.demultiplex(*params.values())
params['overwrite'] = False
with pytest.raises(click.UsageError) as excinfo:
commands.demultiplex(*params.values())
assert 'pass --overwrite as an option' in excinfo.value.message