def test_find_a_ctg_placement_3():
"""
Test empty p_ctg paths. If the primary contig cannot be found, this should
throw an exception.
"""
p_paths = {}
fp_in = StringIO(test_placement_1_a_path_as_text)
a_paths = mod.load_tiling_paths_from_stream(fp_in, contig_lens=None, whitelist_seqs=None)
with pytest.raises(Exception):
result = mod.find_a_ctg_placement(p_paths, a_paths)
def test_find_a_ctg_placement_2():
"""
Test empty a_ctg paths.
"""
fp_in = StringIO(test_placement_1_p_path_as_text)
p_paths = mod.load_tiling_paths_from_stream(fp_in, contig_lens=None, whitelist_seqs=None)
a_paths = {}
result = mod.find_a_ctg_placement(p_paths, a_paths)
assert(len(result.keys()) == 0)
def test_find_a_ctg_placement_3():
"""
Test empty p_ctg paths. If the primary contig cannot be found, this should
throw an exception.
"""
p_paths = {}
fp_in = StringIO(test_placement_1_a_path_as_text)
a_paths = mod.load_tiling_paths_from_stream(fp_in,
contig_lens=None,
whitelist_seqs=None)
with pytest.raises(Exception):
result = mod.find_a_ctg_placement(p_paths, a_paths)
def test_find_a_ctg_placement_2():
"""
Test empty a_ctg paths.
"""
fp_in = StringIO(test_placement_1_p_path_as_text)
p_paths = mod.load_tiling_paths_from_stream(fp_in,
contig_lens=None,
whitelist_seqs=None)
a_paths = {}
result = mod.find_a_ctg_placement(p_paths, a_paths)
assert (len(list(result.keys())) == 0)
def test_find_a_ctg_placement_1():
"""
Normal test case.
The find_a_ctg_placement method expects a valid primary contig tiling path dict and a
valid associate contig tiling path dict as inputs.
Validation of the construction of TilingPath objects is performed in the tests
above; here we take these objects for granted.
"""
fp_in = StringIO(test_placement_1_p_path_as_text)
p_paths = mod.load_tiling_paths_from_stream(fp_in, contig_lens=None, whitelist_seqs=None)
fp_in = StringIO(test_placement_1_a_path_as_text)
a_paths = mod.load_tiling_paths_from_stream(fp_in, contig_lens=None, whitelist_seqs=None)
result = mod.find_a_ctg_placement(p_paths, a_paths)
for key, placement in result.iteritems():
assert(placement == test_placement_1_expected[key])
def test_find_a_ctg_placement_1():
"""
Normal test case.
The find_a_ctg_placement method expects a valid primary contig tiling path dict and a
valid associate contig tiling path dict as inputs.
Validation of the construction of TilingPath objects is performed in the tests
above; here we take these objects for granted.
"""
fp_in = StringIO(test_placement_1_p_path_as_text)
p_paths = mod.load_tiling_paths_from_stream(fp_in,
contig_lens=None,
whitelist_seqs=None)
fp_in = StringIO(test_placement_1_a_path_as_text)
a_paths = mod.load_tiling_paths_from_stream(fp_in,
contig_lens=None,
whitelist_seqs=None)
result = mod.find_a_ctg_placement(p_paths, a_paths)
for key, placement in result.items():
assert (placement == test_placement_1_expected[key])