def test_subreadset_scraps(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
rc = bamSieve.filter_reads(
input_bam=BARCODED_DS,
output_bam=ofn,
whitelist=[74056024])
self.assertEqual(rc, 0)
def _verify():
with openDataSet(ofn, strict=False) as ds_out:
ext_res = ds_out.externalResources[0]
for bam_file in [ext_res.bam, ext_res.scraps]:
with BamReader(bam_file) as bam:
zmws = set([rec.HoleNumber for rec in bam])
self.assertEqual(len(zmws), 1)
self.assertTrue(74056024 in zmws)
_verify()
rc = bamSieve.filter_reads(
input_bam=BARCODED_DS,
output_bam=ofn,
count=1,
seed=12345)
_verify()
rc = bamSieve.filter_reads(
input_bam=BARCODED_DS,
output_bam=ofn,
blacklist=[28901719])
self.assertEqual(rc, 0)
def test_subreadset_scraps(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
rc = bamSieve.filter_reads(input_bam=BARCODED_DS,
output_bam=ofn,
whitelist=[74056024])
self.assertEqual(rc, 0)
def _verify():
with openDataSet(ofn, strict=False) as ds_out:
ext_res = ds_out.externalResources[0]
for bam_file in [ext_res.bam, ext_res.scraps]:
with BamReader(bam_file) as bam:
zmws = set([rec.HoleNumber for rec in bam])
self.assertEqual(len(zmws), 1)
self.assertTrue(74056024 in zmws)
_verify()
rc = bamSieve.filter_reads(input_bam=BARCODED_DS,
output_bam=ofn,
count=1,
seed=12345)
_verify()
rc = bamSieve.filter_reads(input_bam=BARCODED_DS,
output_bam=ofn,
blacklist=[28901719])
self.assertEqual(rc, 0)
def test_error(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(input_bam=DS1,
output_bam=ofn,
whitelist=set([5, 6, 7, 8]),
blacklist=set([1, 2, 3, 4]))
self.assertEqual(rc, 1)
rc = bamSieve.filter_reads(input_bam=DS1,
output_bam=ofn,
whitelist=set([5, 6, 7, 8]),
percentage=50)
self.assertEqual(rc, 1)
rc = bamSieve.filter_reads(input_bam=DS1,
output_bam=ofn,
percentage=500)
self.assertEqual(rc, 1)
rc = bamSieve.filter_reads(input_bam=DS1,
output_bam=ofn,
percentage=50,
count=1)
self.assertEqual(rc, 1)
# dataset output, but BAM input
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
rc = bamSieve.filter_reads(input_bam=SUBREADS2,
output_bam=ofn,
percentage=50)
self.assertEqual(rc, 1)
def test_error(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(
input_bam=DS1,
output_bam=ofn,
whitelist=set([5, 6, 7, 8]),
blacklist=set([1, 2, 3, 4]))
self.assertEqual(rc, 1)
rc = bamSieve.filter_reads(
input_bam=DS1,
output_bam=ofn,
whitelist=set([5, 6, 7, 8]),
percentage=50)
self.assertEqual(rc, 1)
rc = bamSieve.filter_reads(
input_bam=DS1,
output_bam=ofn,
percentage=500)
self.assertEqual(rc, 1)
rc = bamSieve.filter_reads(
input_bam=DS1,
output_bam=ofn,
percentage=50,
count=1)
self.assertEqual(rc, 1)
# dataset output, but BAM input
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
rc = bamSieve.filter_reads(
input_bam=SUBREADS2,
output_bam=ofn,
percentage=50)
self.assertEqual(rc, 1)
def test_whitelist(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
WHITELIST = set([24962, 32901, 30983])
def _run_with_whitelist(wl):
rc = bamSieve.filter_reads(
input_bam=SUBREADS3,
output_bam=ofn,
whitelist=wl)
self.assertEqual(rc, 0)
with openDataFile(ofn, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, WHITELIST)
_run_with_whitelist(WHITELIST)
_run_with_whitelist(",".join([str(x) for x in list(WHITELIST)]))
tmp_wl = tempfile.NamedTemporaryFile(suffix=".txt").name
with open(tmp_wl, "w") as wl_out:
wl_out.write("\n".join([str(x) for x in list(WHITELIST)]))
_run_with_whitelist(tmp_wl)
# now with a BAM file as whitelist
rc = bamSieve.filter_reads(
input_bam=SUBREADS3,
output_bam=ofn,
whitelist=SUBREADS4)
with openDataFile(ofn, strict=False) as bam_out:
self.assertEqual(117, len([rec for rec in bam_out]))
def test_whitelist(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
WHITELIST = set([24962, 32901, 30983])
def _run_with_whitelist(wl):
rc = bamSieve.filter_reads(input_bam=SUBREADS3,
output_bam=ofn,
whitelist=wl)
self.assertEqual(rc, 0)
with BamReader(ofn) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, WHITELIST)
_run_with_whitelist(WHITELIST)
_run_with_whitelist(",".join([str(x) for x in list(WHITELIST)]))
tmp_wl = tempfile.NamedTemporaryFile(suffix=".txt").name
with open(tmp_wl, "w") as wl_out:
wl_out.write("\n".join([str(x) for x in list(WHITELIST)]))
_run_with_whitelist(tmp_wl)
# now with a BAM file as whitelist
rc = bamSieve.filter_reads(input_bam=SUBREADS3,
output_bam=ofn,
whitelist=SUBREADS4)
with BamReader(ofn) as bam_out:
self.assertEqual(117, len([rec for rec in bam_out]))
def _run_with_blacklist(bl):
rc = bamSieve.filter_reads(input_bam=SUBREADS2,
output_bam=ofn,
blacklist=bl)
self.assertEqual(rc, 0)
with BamReader(ofn) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([9]))
def test_anonymize(self):
ofn1 = tempfile.NamedTemporaryFile(suffix=".bam").name
ofn2 = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(input_bam=SUBREADS3,
output_bam=ofn1,
whitelist=set([24962]))
self.assertEqual(rc, 0)
rc = bamSieve.filter_reads(input_bam=SUBREADS3,
output_bam=ofn2,
whitelist=set([24962]),
anonymize=True)
self.assertEqual(rc, 0)
with openDataFile(ofn1) as bam1:
with openDataFile(ofn2) as bam2:
for rec1, rec2 in zip(bam1, bam2):
self.assertEqual(rec1.qName, rec2.qName)
self.assertNotEqual(rec1.peer.seq, rec2.peer.seq)
def _run_with_whitelist(wl):
rc = bamSieve.filter_reads(input_bam=SUBREADS3,
output_bam=ofn,
whitelist=wl)
self.assertEqual(rc, 0)
with BamReader(ofn) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, WHITELIST)
def _run_with_whitelist(wl):
rc = bamSieve.filter_reads(
input_bam=SUBREADS3,
output_bam=ofn,
whitelist=wl)
self.assertEqual(rc, 0)
with openDataFile(ofn, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, WHITELIST)
def _run_with_blacklist(bl):
rc = bamSieve.filter_reads(
input_bam=SUBREADS2,
output_bam=ofn,
blacklist=bl)
self.assertEqual(rc, 0)
with openDataFile(ofn, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([9]))
def test_count(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(input_bam=SUBREADS3,
output_bam=ofn,
count=1,
seed=12345)
self.assertEqual(rc, 0)
with BamReader(ofn) as bam_out:
zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(len(zmws), 1)
def test_barcodes(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(input_bam=BARCODED,
output_bam=ofn,
whitelist=[0],
use_barcodes=True)
with BamReader(ofn) as bam_out:
zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(len(zmws), 1)
self.assertTrue(74056024 in zmws)
def test_anonymize(self):
ofn1 = tempfile.NamedTemporaryFile(suffix=".bam").name
ofn2 = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(
input_bam=SUBREADS3,
output_bam=ofn1,
whitelist=set([24962]))
self.assertEqual(rc, 0)
rc = bamSieve.filter_reads(
input_bam=SUBREADS3,
output_bam=ofn2,
whitelist=set([24962]),
anonymize=True)
self.assertEqual(rc, 0)
with openDataFile(ofn1, strict=False) as bam1:
with openDataFile(ofn2, strict=False) as bam2:
for rec1, rec2 in zip(bam1, bam2):
self.assertEqual(rec1.qName, rec2.qName)
self.assertNotEqual(rec1.peer.seq, rec2.peer.seq)
def test_dataset_io(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
rc = bamSieve.filter_reads(
input_bam=DS2,
output_bam=ofn,
whitelist="8")
self.assertEqual(rc, 0)
with openDataSet(ofn, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([8]))
def test_percentage(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(
input_bam=SUBREADS3,
output_bam=ofn,
percentage=50,
seed=12345)
self.assertEqual(rc, 0)
with BamReader(ofn) as bam_out:
zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(len(zmws), 24)
def test_barcodes(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(
input_bam=BARCODED,
output_bam=ofn,
whitelist=[0],
use_barcodes=True)
with BamReader(ofn) as bam_out:
zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(len(zmws), 1)
self.assertTrue(74056024 in zmws)
def test_count(self):
ofn = tempfile.NamedTemporaryFile(suffix=".bam").name
rc = bamSieve.filter_reads(
input_bam=SUBREADS3,
output_bam=ofn,
count=1,
seed=12345)
self.assertEqual(rc, 0)
with openDataFile(ofn, strict=False) as bam_out:
zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(len(zmws), 1)
def test_dataset_io(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
rc = bamSieve.filter_reads(input_bam=DS2,
output_bam=ofn,
whitelist="8")
self.assertEqual(rc, 0)
with openDataSet(ofn, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([8]))
# make sure paths are absolute
tmpdir = tempfile.mkdtemp()
ofn2 = op.join(tmpdir, op.basename(ofn))
shutil.copyfile(ofn, ofn2)
with openDataSet(ofn2, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([8]))
def test_dataset_io(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
rc = bamSieve.filter_reads(
input_bam=DS2,
output_bam=ofn,
whitelist="8")
self.assertEqual(rc, 0)
with openDataSet(ofn, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([8]))
# make sure paths are absolute
tmpdir = tempfile.mkdtemp()
ofn2 = op.join(tmpdir, op.basename(ofn))
shutil.copyfile(ofn, ofn2)
with openDataSet(ofn2, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([8]))
def test_dataset_relative_paths(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
basename = op.basename(ofn).split(".")[0]
rc = bamSieve.filter_reads(input_bam=DS2,
output_bam=ofn,
whitelist="8",
relative=True)
self.assertEqual(rc, 0)
# move everything to another directory and make sure paths still work
tmpdir = tempfile.mkdtemp()
for file_name in os.listdir(op.dirname(ofn)):
if file_name.startswith(basename):
shutil.move(op.join(op.dirname(ofn), file_name),
op.join(tmpdir, file_name))
ofn2 = op.join(tmpdir, op.basename(ofn))
with openDataSet(ofn2, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([8]))
def test_dataset_relative_paths(self):
ofn = tempfile.NamedTemporaryFile(suffix=".subreadset.xml").name
basename = op.basename(ofn).split(".")[0]
rc = bamSieve.filter_reads(
input_bam=DS2,
output_bam=ofn,
whitelist="8",
relative=True)
self.assertEqual(rc, 0)
# move everything to another directory and make sure paths still work
tmpdir = tempfile.mkdtemp()
for file_name in os.listdir(op.dirname(ofn)):
if file_name.startswith(basename):
shutil.move(op.join(op.dirname(ofn), file_name),
op.join(tmpdir, file_name))
ofn2 = op.join(tmpdir, op.basename(ofn))
with openDataSet(ofn2, strict=False) as bam_out:
have_zmws = set([rec.HoleNumber for rec in bam_out])
self.assertEqual(have_zmws, set([8]))
