def test_main_1(tmpdir, capsys):
"""
Empty input files should produce empty output.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in xrange(500)])
fasta_lines = [
]
tp_lines = [
]
expected_lines = [
]
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = ['prog',
'--a-ctg', str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path', str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines)
assert(out == expected)
def test_main_1(tmpdir, capsys):
"""
Empty input files should produce empty output.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in range(500)])
fasta_lines = []
tp_lines = []
expected_lines = []
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = [
'prog',
'--a-ctg',
str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path',
str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines)
assert (out == expected)
def test_main_4(tmpdir, capsys):
"""
Tiling path does not contain all contigs present in a_ctg.fa. Only the ones
which match should be output, still.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in range(500)])
fasta_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
]
tp_lines = [
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
]
expected_lines = [
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
]
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = [
'prog',
'--a-ctg',
str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path',
str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert (out == expected)
def test_main_4(tmpdir, capsys):
"""
Tiling path does not contain all contigs present in a_ctg.fa. Only the ones
which match should be output, still.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in xrange(500)])
fasta_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
]
tp_lines = [
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
]
expected_lines = [
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
]
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = ['prog',
'--a-ctg', str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path', str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert(out == expected)
def test_main_3(tmpdir, capsys):
"""
Empty tiling path file.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in range(500)])
fasta_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
]
tp_lines = []
expected_lines = []
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = [
'prog',
'--a-ctg',
str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path',
str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines)
assert (out == expected)
def test_main_3(tmpdir, capsys):
"""
Empty tiling path file.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in xrange(500)])
fasta_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
]
tp_lines = [
]
expected_lines = [
]
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = ['prog',
'--a-ctg', str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path', str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines)
assert(out == expected)
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass
def test_main_2(tmpdir, capsys):
"""
Regular test case.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in range(500)])
fasta_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
]
tp_lines = [
'000000F-001-00 000000217:E 000000189:E 000000189 33799 36467 33798 99.97',
'000000F-001-00 000000189:E 000000223:E 000000223 35637 39957 35637 99.96',
'000000F-001-00 000000223:E 000000273:E 000000273 38476 39968 38476 99.96',
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
'000000F-002-00 000000035:E 000000078:E 000000078 38260 39977 38260 99.98',
'000000F-002-00 000000078:E 000000020:E 000000020 38490 39969 38490 99.97',
'000000F-002-00 000000020:E 000000142:E 000000142 39547 39983 39547 99.98',
'000000F-002-01 000000035:E 000000228:E 000000228 38670 39961 38670 99.89',
'000000F-002-01 000000228:E 000000201:E 000000201 38578 39971 38571 99.95',
'000000F-002-01 000000201:E 000000243:E 000000243 39822 39967 39822 99.96',
'000000F-002-02 000000176:E 000000250:E 000000250 39602 39966 39602 99.97',
'000000F-002-02 000000250:E 000000211:E 000000211 38613 39982 38610 99.98',
'000000F-002-02 000000211:E 000000177:E 000000177 39666 39984 39668 99.98',
]
expected_lines = [
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
'000000F-002-02 000000176:E 000000250:E 000000250 39602 39966 39602 99.97',
'000000F-002-02 000000250:E 000000211:E 000000211 38613 39982 38610 99.98',
'000000F-002-02 000000211:E 000000177:E 000000177 39666 39984 39668 99.98',
]
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = [
'prog',
'--a-ctg',
str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path',
str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert (out == expected)
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass
def test_main_2(tmpdir, capsys):
"""
Regular test case.
"""
random.seed(1234567)
dummy_seq = ''.join([random.choice('ACTG') for i in xrange(500)])
fasta_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
]
tp_lines = [
'000000F-001-00 000000217:E 000000189:E 000000189 33799 36467 33798 99.97',
'000000F-001-00 000000189:E 000000223:E 000000223 35637 39957 35637 99.96',
'000000F-001-00 000000223:E 000000273:E 000000273 38476 39968 38476 99.96',
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
'000000F-002-00 000000035:E 000000078:E 000000078 38260 39977 38260 99.98',
'000000F-002-00 000000078:E 000000020:E 000000020 38490 39969 38490 99.97',
'000000F-002-00 000000020:E 000000142:E 000000142 39547 39983 39547 99.98',
'000000F-002-01 000000035:E 000000228:E 000000228 38670 39961 38670 99.89',
'000000F-002-01 000000228:E 000000201:E 000000201 38578 39971 38571 99.95',
'000000F-002-01 000000201:E 000000243:E 000000243 39822 39967 39822 99.96',
'000000F-002-02 000000176:E 000000250:E 000000250 39602 39966 39602 99.97',
'000000F-002-02 000000250:E 000000211:E 000000211 38613 39982 38610 99.98',
'000000F-002-02 000000211:E 000000177:E 000000177 39666 39984 39668 99.98',
]
expected_lines = [
'000000F-001-01 000000217:E 000000110:E 000000110 33829 37916 33802 99.86',
'000000F-001-01 000000110:E 000000037:E 000000037 35944 39971 35947 99.97',
'000000F-001-01 000000037:E 000000131:E 000000131 39313 39968 39313 99.97',
'000000F-002-02 000000176:E 000000250:E 000000250 39602 39966 39602 99.97',
'000000F-002-02 000000250:E 000000211:E 000000211 38613 39982 38610 99.98',
'000000F-002-02 000000211:E 000000177:E 000000177 39666 39984 39668 99.98',
]
# Create a temporary input files.
test_out_a_ctg_file = tmpdir.join('a_ctg.fa')
test_out_a_ctg_file.write('\n'.join(fasta_lines))
test_out_a_ctg_all_tp_file = tmpdir.join('a_ctg_all_tiling_path')
test_out_a_ctg_all_tp_file.write('\n'.join(tp_lines) + '\n')
# test_out_a_ctg_all_tp_file.write('\n')
argv = ['prog',
'--a-ctg', str(test_out_a_ctg_file),
'--a-ctg-all-tiling-path', str(test_out_a_ctg_all_tp_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert(out == expected)