def run_fragments(options):
"""Wraps the sctools.fragments function for use on the command line
"""
fragments.fragments(bam=options.bam,
fragment_path=options.fragments,
min_mapq=options.min_mapq,
nproc=options.nproc,
cellbarcode=options.barcodetag,
readname_barcode=options.barcode_regex,
chromosomes=options.use_chrom,
cells=options.cells,
max_distance=options.max_distance)
def run_fragments(options):
"""Wraps the sctools.fragments function for use on the command line
"""
fragments.fragments(bam=options.bam,
fragment_path=options.fragments,
min_mapq=options.min_mapq,
nproc=options.nproc,
cellbarcode=options.barcodetag,
readname_barcode=options.barcode_regex,
chromosomes=options.use_chrom,
cells=options.cells,
max_distance=options.max_distance,
min_distance=options.min_distance,
chunksize=options.chunksize,
shifts=[options.shift_plus, options.shift_minus],
collapse_within=options.collapse_within)
def test_fragments(tmpdir, collapse_within):
basepath = os.path.dirname(os.path.realpath(__file__))
bam = os.path.join(basepath, "data/test.bam")
outf = tmpdir / "frags.bed"
fragments.fragments(
bam=bam,
fragment_path=outf,
collapse_within=collapse_within,
)
output = [line.strip("\n") for line in open(outf, "r")]
if collapse_within:
expected_path = os.path.join(basepath, "data/frags_within.bed")
else:
expected_path = os.path.join(basepath, "data/frags_across.bed")
expected = [line.strip("\n") for line in open(expected_path, "r")]
output.sort()
expected.sort()
assert output == expected