def test_main_1(tmpdir, capsys):
# test_dir = os.path.join(helpers.get_test_data_dir(), 'gfa-1')
gfa_graph = mod.GFAGraph()
gfa_graph.add_node('node1', 7, 'ACTGAAA', tags={}, labels={})
gfa_graph.add_node('node2', 10, 'AAACCCGGGT', tags={}, labels={})
gfa_graph.add_edge('edge1', 'node1', '+', 'node2', '+', 4, 7, 0, 3, '*', tags={}, labels={})
gfa_graph.add_path('000000F', ['node1', 'node2'], ['4M', '7M'], tags={}, labels={})
gfa_json_file = tmpdir.join('graph.gfa.json')
gfa_json_file.write(mod.serialize_gfa(gfa_graph))
argv = ['prog',
str(gfa_json_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = """H VN:Z:1.0
S node1 ACTGAAA LN:i:7
S node2 AAACCCGGGT LN:i:10
L node1 + node2 + 3M
P 000000F node1,node2 4M,7M
"""
# Custom tags can be in an arbitrary order and hard to compare.
# They might also change between versions, so just remove
# them manually here and compare only the important fields.
result = []
for line in out.splitlines():
line = line.strip()
sl = line.split()
if len(line) == 0:
continue
if line[0] == 'H':
result.append('\t'.join(sl[0:2]))
elif line[0] == 'S':
result.append('\t'.join(sl[0:4]))
elif line[0] == 'L':
result.append('\t'.join(sl[0:6]))
elif line[0] == 'P':
result.append('\t'.join(sl[0:4]))
result_str = '\n'.join(result) + '\n'
assert(result_str == expected)
def test_main_6(capsys):
test_dir = os.path.join(helpers.get_test_data_dir(), 'gfa-1')
argv = [
'prog',
'--p-ctg-tiling-path',
os.path.join(test_dir, 'p_ctg_tiling_path'),
'--a-ctg-tiling-path',
os.path.join(test_dir, 'a_ctg_tiling_path'),
'--preads-fasta',
os.path.join(test_dir, 'preads4falcon.fasta'),
'--p-ctg-fasta',
os.path.join(test_dir, 'p_ctg.fa'),
'--a-ctg-fasta',
os.path.join(test_dir, 'a_ctg.fa'),
'--sg-edges-list',
os.path.join(test_dir, 'sg_edges_list'),
'--utg-data',
os.path.join(test_dir, 'utg_data'),
'--ctg-paths',
os.path.join(test_dir, 'ctg_paths'),
'--tiling',
# '--write-reads',
# '--write-contigs',
'--min-p-len',
'10000',
'--min-a-len',
'10000',
]
mod.main(argv)
out, err = capsys.readouterr()
result = out.strip().splitlines()
expected = [
line.strip() for line in
open(os.path.join(
test_dir, 'expected-6-tiling-no_r-no_c-minlen.gfa')).readlines()
]
assert (result == expected)
def test_main_2(capsys):
test_dir = os.path.join(helpers.get_test_data_dir(), 'gfa-1')
argv = ['prog',
'--p-ctg-tiling-path', os.path.join(test_dir, 'p_ctg_tiling_path'),
'--a-ctg-tiling-path', os.path.join(test_dir, 'a_ctg_tiling_path'),
'--preads-fasta', os.path.join(test_dir, 'preads4falcon.fasta'),
'--p-ctg-fasta', os.path.join(test_dir, 'p_ctg.fa'),
'--a-ctg-fasta', os.path.join(test_dir, 'a_ctg.fa'),
'--sg-edges-list', os.path.join(test_dir, 'sg_edges_list'),
'--utg-data', os.path.join(test_dir, 'utg_data'),
'--ctg-paths', os.path.join(test_dir, 'ctg_paths'),
# '--add-string-graph',
'--write-reads',
'--write-contigs',
'--min-p-len', '0',
'--min-a-len', '0',
]
mod.main(argv)
out, err = capsys.readouterr()
expected_path = os.path.join(test_dir,
'expected-2-tiling-r-c.gfa')
helpers.assert_filecmp(out, expected_path)
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass
