def test_anno_1(tmpdir):
"test --simple version"
make_bam(
tmpdir.strpath, """
123456789_123456789_12
r1 + ...........
r1 - ......*....
r2 + .........*.
r2 - .....*.......
r3 + ...........
r3 - ....*......
r4 + ...........
r4 - ...........
123456789_123456789_12
""")
sam = AlignmentFile(tmpdir.join("test.bam").strpath)
o = Namespace(
query=tmpdir.join("test.vcf").strpath,
cfdna=sam,
gdna=None,
simple=True,
verbos=False,
fast=False,
qual=20,
output=tmpdir.join("test_MrBam.vcf").strpath,
allow_inconsist=False,
mismatch_limit=-1,
)
anno(o)
for i in open(tmpdir.join("test_MrBam.vcf").strpath):
if i.startswith('#'):
continue
i = i.split('\t')
if i[1] == '12':
a, b, c, d = i[-1].split(':')[-1].strip().split(',')
assert a == '0'
assert b == '0'
assert c == '1'
assert d == '1'
elif i[1] == '16':
a, b, c, d = i[-1].split(':')[-1].strip().split(',')
assert a == '0'
assert b == '0'
assert c == '0'
assert d == '0'
else:
raise Exception("unexpected variant call")
def test_pad_softclip_1(tmpdir):
"it should memorize the result"
make_bam(tmpdir.strpath, """
r1 + __.*.......
r1 - .*.......__
""")
o = Namespace(verbos=False, mismatch_limit=-1)
sam = AlignmentFile(tmpdir.join("test.bam").strpath)
a = pad_softclip(sam)
b = pad_softclip(sam)
assert a is b
def test_pad_softclip_3(tmpdir):
"it should pad softclipped bases"
make_bam(
tmpdir.strpath, """
123456789_123
r1 + __.*.......
r1 - .*.........
r2 - ...*.......
r2 + .*.......__
""")
o = Namespace(verbos=False, mismatch_limit=-1)
sam = AlignmentFile(tmpdir.join("test.bam").strpath)
adjusted_pos = pad_softclip(sam)
assert adjusted_pos["r1"] == (0, 13) # 0-based position
assert adjusted_pos["r2"] == (0, 13)
def test_pad_softclip_2(tmpdir):
"it should ignore more than two reads which share the same name"
make_bam(
tmpdir.strpath, """
r1 + __.*.......
r1 - .*.......__
r1 - .*.......__
r2 + .*.......__
r2 - .*.......__
""")
o = Namespace(verbos=False, mismatch_limit=-1)
sam = AlignmentFile(tmpdir.join("test.bam").strpath)
adjusted_pos = pad_softclip(sam)
assert sum(1 for startpos, length in adjusted_pos.values()
if startpos != -1) == 1
def test_init_3(tmpdir):
"it should generate a proper output file name if not provided"
make_bam(
tmpdir.strpath, """
123456789_123456789_
r1 + ...........
r1 - ......*....
r2 + .........*.
r2 - .....*.......
""")
o = Namespace(query="test.vcf",
cfdna=tmpdir.join("test.bam").strpath,
gdna=None,
output=None)
init(o)
assert o.output != None
def test_init_2(tmpdir):
"it should open sam file if provided"
make_bam(
tmpdir.strpath, """
123456789_123456789_
r1 + ...........
r1 - ......*....
r2 + .........*.
r2 - .....*.......
""")
o = Namespace(query="test.vcf",
cfdna=tmpdir.join("test.bam").strpath,
gdna=None,
output=None)
init(o)
assert isinstance(o.cfdna, AlignmentFile)
assert o.gdna == None
def test_get_reads_1(tmpdir):
"it should get all but only the reads that covers the given position"
make_bam(
tmpdir.strpath, """
123456789_123456789_12
r1 + ...........
r1 - ......*....
r2 + .........*.
r2 - .....*.......
r3 + ...........
r3 - ....*......
r4 + ...........
r4 - ...........
123456789_123456789_12
""")
o = Namespace(verbos=False, mismatch_limit=-1)
sam = AlignmentFile(tmpdir.join("test.bam").strpath)
assert sum(1 for _ in get_reads(o, sam, 'ref', '4')) == 2
assert sum(1 for _ in get_reads(o, sam, 'ref', '12')) == 7
assert sum(1 for _ in get_reads(o, sam, 'ref', '20')) == 2
def test_get_reads_2(tmpdir):
"it should read properties correctly"
make_bam(
tmpdir.strpath, """
123456789_123
r1 + ...*.......
r1 - .*.........
""")
o = Namespace(verbos=False, mismatch_limit=-1)
sam = AlignmentFile(tmpdir.join("test.bam").strpath)
r = next(get_reads(o, sam, 'ref', '4'))
assert r[0] == "r1" # name
assert r[3] == 0 # 0-based pos
assert r[4] == 11 # length
assert r[5] == -1 # mismatch, not caculated
assert r[6] == 2 # mate pos
assert r[7] == 13 # template length
assert r[8] == False # is_reverse
assert r[9] == True # paired and mapped