def test_process_bam_raises():
bam = os.path.join(DATA, "no_umi.bam")
tbam = os.path.join(DATA, "tmp.bam")
with captured_output() as (o, e):
process_bam(bam, tbam)
if os.path.exists(tbam):
os.remove(tbam)
def test_process_bam_raises():
bam = os.path.join(DATA, "no_umi.bam")
tbam = os.path.join(DATA, "tmp.bam")
with captured_output() as (o, e):
process_bam(bam, tbam)
if os.path.exists(tbam):
os.remove(tbam)
def test_process_bam_mismatches():
tbam = os.path.join(DATA, "tmp.bam")
bam = os.path.join(DATA, "ordered_umi.bam")
if os.path.exists(tbam):
os.remove(tbam)
with captured_output() as (out, err):
process_bam(bam, tbam, mismatches=1)
assert os.path.exists(tbam)
it = iter(out.getvalue().split("\n"))
assert it.next().strip() == "1\t9\t10\t4\t2"
assert it.next().strip() == "1\t11\t12\t2\t1"
assert it.next().strip() == "1\t29\t30\t2\t1"
bam_reader = Samfile(tbam)
it = iter(bam_reader)
r = it.next()
assert r.pos == 4
assert r.qname == "read8:UMI_ATTCAGGG"
r = it.next()
assert r.pos == 9
assert r.qname == "read1:UMI_AAAAAGGG"
r = it.next()
assert r.pos == 9
assert r.qname == "read4:UMI_AAAGGGGG"
r = it.next()
assert r.pos == 11
assert r.qname == "read5:UMI_ATTTAGGG"
bam_reader.close()
os.remove(tbam)
def test_process_bam_mismatches():
tbam = os.path.join(DATA, "tmp.bam")
bam = os.path.join(DATA, "ordered_umi.bam")
if os.path.exists(tbam):
os.remove(tbam)
with captured_output() as (out, err):
process_bam(bam, tbam, mismatches=1)
assert os.path.exists(tbam)
it = iter(out.getvalue().split("\n"))
assert it.next().strip() == "1\t9\t10\t4\t2"
assert it.next().strip() == "1\t11\t12\t2\t1"
assert it.next().strip() == "1\t29\t30\t2\t1"
bam_reader = Samfile(tbam)
it = iter(bam_reader)
r = it.next()
assert r.pos == 4
assert r.qname == "read8:UMI_ATTCAGGG"
r = it.next()
assert r.pos == 9
assert r.qname == "read1:UMI_AAAAAGGG"
r = it.next()
assert r.pos == 9
assert r.qname == "read4:UMI_AAAGGGGG"
r = it.next()
assert r.pos == 11
assert r.qname == "read5:UMI_ATTTAGGG"
bam_reader.close()
os.remove(tbam)
