def test_main_2(tmpdir, capsys):
"""
Aligning very long sequences should work fine with linear-memory aligners (e.g. Edlib).
Using the legacy alignment (align_dw.py) would fail on this test.
"""
random.seed(1234567)
# Generate a dummy sequence.
dummy_seq = ''.join([random.choice('ACTG') for i in range(300000)])
fasta_lines = [
# Base sequence.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
# Exactly the same sequence as a duplicate branch.
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq
]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = [
'prog',
'--a-ctg-all',
str(test_out_a_ctg_all_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = ''
assert (out == expected)
def test_main_2(tmpdir, capsys):
"""
Aligning very long sequences should work fine with linear-memory aligners (e.g. Edlib).
Using the legacy alignment (align_dw.py) would fail on this test.
"""
random.seed(1234567)
# Generate a dummy sequence.
dummy_seq = ''.join([random.choice('ACTG') for i in xrange(300000)])
fasta_lines = [
# Base sequence.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
# Exactly the same sequence as a duplicate branch.
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = ['prog',
'--a-ctg-all', str(test_out_a_ctg_all_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = ''
assert(out == expected)
def test_main_3(tmpdir, capsys):
"""
Test deduplication on very short sequences.
The legacy deduplication code had a 2000bp threshold on minimum sequence
length for alignment. If any of the sequences was shorter than this,
the alignment wouldn't be performed, and the sequence would not be deduplicated
even if it was a duplicate.
This tests for the same behaviour as the legacy code.
The deduplication is designed as "conservative": keep the sequences unless
there is strong evidence of duplication.
TODO: Reconsider this logic.
"""
random.seed(1234567)
# Generate a dummy sequence.
dummy_seq = ''.join([random.choice('ACTG') for i in range(300)])
fasta_lines = [
# Base sequence.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
# Exactly the same sequence as a duplicate branch.
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq
]
expected_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 0.00 0.00',
dummy_seq,
]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = [
'prog',
'--a-ctg-all',
str(test_out_a_ctg_all_file),
'--min-seq-len',
'2000',
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert (out == expected)
def test_main_1(tmpdir, capsys):
random.seed(1234567)
dummy_seq_001_00 = ''.join([random.choice('ACTG') for i in range(45000)])
dummy_seq_001_01 = dummy_seq_001_00[0:20000] + dummy_seq_001_00[25000:]
dummy_seq_002_00 = dummy_seq_001_00
dummy_seq_002_01 = dummy_seq_001_01
dummy_seq_002_02 = dummy_seq_002_01
fasta_lines = [
# This tests plain deduplication. The 001-01 is not a duplicate.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_001_00,
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_001_01,
'>000000F-002-00 000000218:E 000000057:E 46974 1268418 33 0 1.00 1.00',
# This tests deduplication of 002-02 vs 002-01. The 002-02 should be removed.
dummy_seq_002_00,
'>000000F-002-01 000000124:E 000000079:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_002_01,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_002_02,
]
expected_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 -5000 1.00 0.50',
dummy_seq_001_01,
'>000000F-002-01 000000124:E 000000079:E 46974 1268418 33 -5000 1.00 0.50',
dummy_seq_002_01,
]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = [
'prog',
'--a-ctg-all',
str(test_out_a_ctg_all_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert (out == expected)
def test_main_4(tmpdir, capsys):
"""
Align two completely different sequences.
The legacy alignment (align_dw.py) would fail on this test, as it would
(unsuccessfuly) try to map one sequence to another, and then align
in that range. Since the sequences are completely different,
such mapping wouldn't be possible.
However, the sequences should globally be aligned (coverage 1.00), with identity 0.00.
The align_edlib.py returns the correct expected result.
"""
random.seed(1234567)
# Generate a dummy sequence.
dummy_seq_1 = ''.join([random.choice('AC') for i in range(3000)])
dummy_seq_2 = ''.join([random.choice('GT') for i in range(3000)])
fasta_lines = [
# Base sequence.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_1,
# Exactly the same sequence as a duplicate branch.
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_2
]
expected_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 0.00 0.00',
dummy_seq_2,
]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = [
'prog',
'--a-ctg-all',
str(test_out_a_ctg_all_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert (out == expected)
def test_main_3(tmpdir, capsys):
"""
Test deduplication on very short sequences.
The legacy deduplication code had a 2000bp threshold on minimum sequence
length for alignment. If any of the sequences was shorter than this,
the alignment wouldn't be performed, and the sequence would not be deduplicated
even if it was a duplicate.
This tests for the same behaviour as the legacy code.
The deduplication is designed as "conservative": keep the sequences unless
there is strong evidence of duplication.
TODO: Reconsider this logic.
"""
random.seed(1234567)
# Generate a dummy sequence.
dummy_seq = ''.join([random.choice('ACTG') for i in xrange(300)])
fasta_lines = [
# Base sequence.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq,
# Exactly the same sequence as a duplicate branch.
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq
]
expected_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 0.00 0.00',
dummy_seq,
]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = ['prog',
'--a-ctg-all', str(test_out_a_ctg_all_file),
'--min-seq-len', '2000',
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert(out == expected)
def test_main_1(tmpdir, capsys):
random.seed(1234567)
dummy_seq_001_00 = ''.join([random.choice('ACTG') for i in xrange(45000)])
dummy_seq_001_01 = dummy_seq_001_00[0:20000] + dummy_seq_001_00[25000:]
dummy_seq_002_00 = dummy_seq_001_00
dummy_seq_002_01 = dummy_seq_001_01
dummy_seq_002_02 = dummy_seq_002_01
fasta_lines = [
# This tests plain deduplication. The 001-01 is not a duplicate.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_001_00,
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_001_01,
'>000000F-002-00 000000218:E 000000057:E 46974 1268418 33 0 1.00 1.00',
# This tests deduplication of 002-02 vs 002-01. The 002-02 should be removed.
dummy_seq_002_00,
'>000000F-002-01 000000124:E 000000079:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_002_01,
'>000000F-002-02 000000125:E 000000080:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_002_02,
]
expected_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 -5000 1.00 0.50',
dummy_seq_001_01,
'>000000F-002-01 000000124:E 000000079:E 46974 1268418 33 -5000 1.00 0.50',
dummy_seq_002_01,
]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = ['prog',
'--a-ctg-all', str(test_out_a_ctg_all_file),
]
mod.main(argv)
out, err = capsys.readouterr()
expected = '\n'.join(expected_lines) + '\n'
assert(out == expected)
def test_main_4(tmpdir, capsys):
"""
Align two completely different sequences.
The legacy alignment (align_dw.py) would fail on this test, as it would
(unsuccessfuly) try to map one sequence to another, and then align
in that range. Since the sequences are completely different,
such mapping wouldn't be possible.
However, the sequences should globally be aligned (coverage 1.00), with identity 0.00.
The align_edlib.py returns the correct expected result.
"""
random.seed(1234567)
# Generate a dummy sequence.
dummy_seq_1 = ''.join([random.choice('AC') for i in xrange(3000)])
dummy_seq_2 = ''.join([random.choice('GT') for i in xrange(3000)])
fasta_lines = [
# Base sequence.
'>000000F-001-00 000000217:E 000000056:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_1,
# Exactly the same sequence as a duplicate branch.
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 1.00 1.00',
dummy_seq_2
]
expected_lines = [
'>000000F-001-01 000000123:E 000000078:E 46974 1268418 33 0 0.00 0.00',
dummy_seq_2,
]
# Create a temporary a_ctg_all.fa file.
test_out_a_ctg_all_file = tmpdir.join('a_ctg_all.fa')
test_out_a_ctg_all_file.write('\n'.join(fasta_lines))
argv = ['prog',
'--a-ctg-all', str(test_out_a_ctg_all_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
from __future__ import absolute_import
from falcon_kit.mains.dedup_a_tigs import main
import sys
if __name__ == "__main__":
main(sys.argv)
def test_help():
try:
mod.main(['prog', '--help'])
except SystemExit:
pass
from falcon_kit.mains.dedup_a_tigs import main
import sys
if __name__ == "__main__":
main(*sys.argv)
