def test_main_4(tmpdir, capsys):
"""
Test for an empty input.
"""
p_ctg_file = tmpdir.join('p_ctg.fa')
p_tp_file = tmpdir.join('p_ctg_tiling_path')
a_tp_file = tmpdir.join('a_ctg_tiling_path')
a_ctg_file = tmpdir.join('a_ctg.fa')
p_ctg_file.write('')
p_tp_file.write('')
a_tp_file.write('')
a_ctg_file.write('')
expected = {'nodes': {}, 'edges': {}, 'paths': {}}
argv = ['prog',
'--p-ctg-tiling-path', str(p_tp_file),
'--a-ctg-tiling-path', str(a_tp_file),
'--p-ctg-fasta', str(p_ctg_file),
'--a-ctg-fasta', str(a_ctg_file),
# '--write-contigs',
'--min-p-len', '0',
'--min-a-len', '0',
# '--only-these-contigs'
]
mod.main(argv)
out, err = capsys.readouterr()
result = json.loads(out)
assert(result == expected)
def test_main_2(tmpdir, capsys):
"""
Test output with sequences.
"""
p_ctg_file = tmpdir.join('p_ctg.fa')
p_tp_file = tmpdir.join('p_ctg_tiling_path')
a_tp_file = tmpdir.join('a_ctg_tiling_path')
a_ctg_file = tmpdir.join('a_ctg.fa')
all_seqs, p_ctg_tps, a_ctg_tps, expected = setup_test(p_ctg_file, p_tp_file, a_ctg_file, a_tp_file)
# This test expects that the nodes are initialized with sequences, so
# set the reference to the generated sequences here.
for key, node in expected['nodes'].iteritems():
node['seq'] = all_seqs[key]
argv = ['prog',
'--p-ctg-tiling-path', str(p_tp_file),
'--a-ctg-tiling-path', str(a_tp_file),
'--p-ctg-fasta', str(p_ctg_file),
'--a-ctg-fasta', str(a_ctg_file),
'--write-contigs',
'--min-p-len', '0',
'--min-a-len', '0',
# '--only-these-contigs'
]
mod.main(argv)
out, err = capsys.readouterr()
result = json.loads(out)
assert(result == expected)
def test_main_1(tmpdir, capsys):
"""
Test without writing contig sequences.
"""
p_ctg_file = tmpdir.join('p_ctg.fa')
p_tp_file = tmpdir.join('p_ctg_tiling_path')
a_tp_file = tmpdir.join('a_ctg_tiling_path')
a_ctg_file = tmpdir.join('a_ctg.fa')
all_seqs, p_ctg_tps, a_ctg_tps, expected = setup_test(p_ctg_file, p_tp_file, a_ctg_file, a_tp_file)
argv = ['prog',
'--p-ctg-tiling-path', str(p_tp_file),
'--a-ctg-tiling-path', str(a_tp_file),
'--p-ctg-fasta', str(p_ctg_file),
'--a-ctg-fasta', str(a_ctg_file),
# '--write-contigs',
'--min-p-len', '0',
'--min-a-len', '0',
# '--only-these-contigs'
]
mod.main(argv)
out, err = capsys.readouterr()
result = json.loads(out)
assert(result == expected)
def test_main_3(tmpdir, capsys):
"""
Test the whitelist.
"""
p_ctg_file = tmpdir.join('p_ctg.fa')
p_tp_file = tmpdir.join('p_ctg_tiling_path')
a_tp_file = tmpdir.join('a_ctg_tiling_path')
a_ctg_file = tmpdir.join('a_ctg.fa')
all_seqs, p_ctg_tps, a_ctg_tps, expected = setup_test(
p_ctg_file, p_tp_file, a_ctg_file, a_tp_file)
only_these_contigs = set(['000002F'])
whitelist_file = tmpdir.join('only_these_contigs')
whitelist_file.write('\n'.join(only_these_contigs) + '\n')
# Adjust the expected results.
# Remove any node not in the whitelist.
blacklist_nodes = [
key for key in (list(p_ctg_tps.keys()) + list(a_ctg_tps.keys()))
if key not in only_these_contigs
]
for key in blacklist_nodes:
expected['nodes'].pop(key, None)
# Remove any edge not in the whitelist.
blacklist_edges = [
key for key, edge in expected['edges'].items()
if edge['v'] not in only_these_contigs
or edge['w'] not in only_these_contigs
]
for key in blacklist_edges:
expected['edges'].pop(key, None)
argv = [
'prog',
'--p-ctg-tiling-path',
str(p_tp_file),
'--a-ctg-tiling-path',
str(a_tp_file),
'--p-ctg-fasta',
str(p_ctg_file),
'--a-ctg-fasta',
str(a_ctg_file),
# '--write-contigs',
'--min-p-len',
'0',
'--min-a-len',
'0',
'--only-these-contigs',
str(whitelist_file),
]
mod.main(argv)
out, err = capsys.readouterr()
result = json.loads(out)
assert (result == expected)
def test_main_3(tmpdir, capsys):
"""
Test the whitelist.
"""
p_ctg_file = tmpdir.join('p_ctg.fa')
p_tp_file = tmpdir.join('p_ctg_tiling_path')
a_tp_file = tmpdir.join('a_ctg_tiling_path')
a_ctg_file = tmpdir.join('a_ctg.fa')
all_seqs, p_ctg_tps, a_ctg_tps, expected = setup_test(p_ctg_file, p_tp_file, a_ctg_file, a_tp_file)
only_these_contigs = set(['000002F'])
whitelist_file = tmpdir.join('only_these_contigs')
whitelist_file.write('\n'.join(only_these_contigs) + '\n')
# Adjust the expected results.
# Remove any node not in the whitelist.
blacklist_nodes = [key for key in (p_ctg_tps.keys() + a_ctg_tps.keys()) if key not in only_these_contigs]
for key in blacklist_nodes:
expected['nodes'].pop(key, None)
# Remove any edge not in the whitelist.
blacklist_edges = [key for key, edge in expected['edges'].iteritems() if edge['v'] not in only_these_contigs or edge['w'] not in only_these_contigs]
for key in blacklist_edges:
expected['edges'].pop(key, None)
argv = ['prog',
'--p-ctg-tiling-path', str(p_tp_file),
'--a-ctg-tiling-path', str(a_tp_file),
'--p-ctg-fasta', str(p_ctg_file),
'--a-ctg-fasta', str(a_ctg_file),
# '--write-contigs',
'--min-p-len', '0',
'--min-a-len', '0',
'--only-these-contigs', str(whitelist_file),
]
mod.main(argv)
out, err = capsys.readouterr()
result = json.loads(out)
assert(result == expected)
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass