def test_read_index():
assert_true(os.path.exists(_sidx))
ibbr = IndexByReadId(_s)
idx = ibbr.read_index()
#import pdb; pdb.set_trace()
assert_true(isinstance(ibbr.idx, OrderedDict))
assert_equal(ibbr.n_records, 1010)
def test_first_last():
ibbr = IndexByReadId(_s)
first_last = ("SRR043348.1017172", "SRR043396.9722121")
for t in first_last:
hits = ibbr.get_reads_by_id(t)
n = 0
for h in hits:
n += 1
assert_equal(t, h.query_name)
assert_equal(n, 2)
def _find_targets(f, targets, expect):
ibbr = IndexByReadId(f)
ibbr.read_index()
for t in targets:
hits = ibbr.get_reads_by_id(t)
n = 0
for h in hits:
n += 1
assert_equal(t, h.query_name)
assert_equal(n, expect)
def test_sort_creates_index():
if os.path.exists(_sidx):
os.remove(_sidx)
ibbr = IndexByReadId(_f)
ibbr.sort_bam(outfile=_s, batch_size=100)
assert_equal(ibbr.bam, _s)
assert_equal(ibbr.index_file, _sidx)
ibbr.create_index()
t = "SRR043372.11318637"
hits = ibbr.get_reads_by_id(t)
n = 0
for h in hits:
n += 1
assert_equal(t, h.query_name)
assert_equal(n, 2)
def test_create_index():
if os.path.exists(_sidx):
os.remove(_sidx)
assert_false(os.path.exists(_sidx))
ibbr = IndexByReadId(_s)
ibbr.create_index(chunk_size=100)
assert_true(os.path.exists(_sidx))
ibbr2 = IndexByReadId(_s2)
ibbr2.create_index()
assert_true(os.path.exists(_s2idx))
sibbr = IndexByReadId(_ssam)
sibbr.create_index(chunk_size=100)
cribbr = IndexByReadId(_scram)
assert_raises(NotImplementedError, cribbr.create_index)
def test_unsorted_error():
ibbr = IndexByReadId(_f)
assert_raises(UnsortedBamError, ibbr.create_index)
def test_sort_input():
for f in [_s, _s2, _sidx, _s2idx]:
if os.path.exists(f):
os.remove(f)
ibbr = IndexByReadId(_f)
ibbr.sort_bam(outfile=_s, batch_size=100)
ibbr2 = IndexByReadId(_f2)
ibbr2.sort_bam()
assert_true(os.path.exists(_s2))
ibbr.sort_bam(outfile=_scram, batch_size=100)
ibbr.sort_bam(outfile=_ssam, batch_size=100)
def test_non_existent():
ibbr = IndexByReadId(_s2)
hits = ibbr.get_reads_by_id( #search for non-existent read
"NZ_GG703879.1_967999_968061_0_1_0_0_4:0:0_1:0:0_62bb")
assert_equal(len(hits), 0)