def test_swap(self):
''' test swap'''
l_in = ['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry']
l_out = ['2', '200', '1', '100', '202', '101', '42.42', '456', '123', '-1', '0', 'qry', 'ref']
a_in = alignment.Alignment('\t'.join(l_in))
a_in._swap()
self.assertEqual(a_in, alignment.Alignment('\t'.join(l_out)))
a_in._swap()
self.assertEqual(a_in, alignment.Alignment('\t'.join(l_in)))
def test_reverse_query(self):
'''Test reverse_query'''
aln = alignment.Alignment('\t'.join([
'100', '142', '1', '42', '43', '42', '100.00', '150', '100', '1',
'1', 'ref', 'qry'
]))
expected = alignment.Alignment('\t'.join([
'100', '142', '100', '59', '43', '42', '100.00', '150', '100', '1',
'1', 'ref', 'qry'
]))
aln.reverse_query()
self.assertEqual(expected, aln)
def test_intersects_variant(self):
'Test intersects_variant'''
snp0 = snp.Snp('100\tA\t.\t600\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry') #100 in ref, 600 in qry
indel = variant.Variant(snp0)
aln1 = alignment.Alignment('100\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
aln2 = alignment.Alignment('101\t500\t600\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
aln3 = alignment.Alignment('100\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
aln4 = alignment.Alignment('101\t500\t601\t1000\t501\t501\t100.00\t600\t1700\t1\t1\tref\tqry')
self.assertTrue(aln1.intersects_variant(indel))
self.assertFalse(aln2.intersects_variant(indel))
self.assertFalse(aln3.intersects_variant(indel))
self.assertFalse(aln4.intersects_variant(indel))
def test_str(self):
'''Test __str__'''
l_in = ['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry']
# the 10th column (counting from zero) is ignored and so not output by __str__
l_out = l_in[:10] + l_in[11:]
a = alignment.Alignment('\t'.join(l_in))
self.assertEqual(str(a), '\t'.join(l_out))
def test_is_self_hit(self):
'''Test is_self_hit'''
tests = [
('\t'.join([
'1', '100', '1', '100', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref'
]), True),
('\t'.join([
'1', '101', '1', '100', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref'
]), False),
('\t'.join([
'2', '100', '1', '100', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref'
]), False),
('\t'.join([
'1', '100', '1', '100', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref2'
]), False),
('\t'.join([
'1', '100', '1', '100', '100', '100', '99.9', '1000', '1000',
'1', '1', 'ref', 'ref'
]), False),
]
for t in tests:
a = alignment.Alignment(t[0])
self.assertEqual(a.is_self_hit(), t[1])
def test_ref_coords(self):
'''Test ref_coords'''
hits = ['\t'.join(['1', '100', '1', '100', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref']),
'\t'.join(['100', '1', '100', '1', '100', '100', '100.00', '1000', '1000', '1', '1', 'ref', 'ref'])
]
for h in hits:
a = alignment.Alignment(h)
self.assertEqual(pyfastaq.intervals.Interval(0,99), a.ref_coords())
def test_qry_coords_from_ref_coord_test_bad_ref_coord(self):
'''Test qry_coords_from_ref_coord with bad ref coords'''
aln = alignment.Alignment('\t'.join(['100', '200', '1', '100', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry']))
with self.assertRaises(alignment.Error):
got = aln.qry_coords_from_ref_coord(98, [])
with self.assertRaises(alignment.Error):
got = aln.qry_coords_from_ref_coord(200, [])
def test_to_msp_crunch(self):
'''Test to_msp_crunch'''
l_in = [
'100', '110', '1', '10', '10', '11', '80.00', '123', '456', '-1',
'0', 'ref', 'qry'
]
a = alignment.Alignment('\t'.join(l_in))
expected = '8 80.00 1 10 qry 100 110 ref'
self.assertEqual(expected, a.to_msp_crunch())
def test_ref_coords_from_qry_coord_when_variant_not_in_nucmer_match(self):
'''Test ref_coords_from_qry_coord when variant not in nucmer match'''
aln = alignment.Alignment('1\t606\t596\t1201\t606\t606\t100.00\t606\t1700\t1\t1\tref\tqry')
snp0 = snp.Snp('127\tA\t.\t77\t75\t77\t1\t0\t606\t1700\t1\t1\tref\tqry')
indel = variant.Variant(snp0)
self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, []))
self.assertEqual((0, False), aln.ref_coords_from_qry_coord(595, [indel]))
self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, []))
self.assertEqual((400, False), aln.ref_coords_from_qry_coord(995, [indel]))
self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, []))
self.assertEqual((605, False), aln.ref_coords_from_qry_coord(1200, [indel]))
def reader(fname):
'''Helper function to open the results file (coords file) and create alignment objects with the values in it'''
f = pyfastaq.utils.open_file_read(fname)
for line in f:
if line.startswith('[') or (not '\t' in line):
continue
yield alignment.Alignment(line)
pyfastaq.utils.close(f)
def test_on_same_strand(self):
'''test on_same_strand'''
self.assertTrue(
alignment.Alignment('\t'.join([
'1', '100', '1', '100', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref'
])).on_same_strand())
self.assertTrue(
alignment.Alignment('\t'.join([
'100', '1', '100', '1', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref'
])).on_same_strand())
self.assertFalse(
alignment.Alignment('\t'.join([
'1', '100', '100', '1', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref'
])).on_same_strand())
self.assertFalse(
alignment.Alignment('\t'.join([
'100', '1', '1', '100', '100', '100', '100.00', '1000', '1000',
'1', '1', 'ref', 'ref'
])).on_same_strand())
def test_qry_coords_from_ref_coord_test_different_strand(self):
'''Test qry_coords_from_ref_coord on different strand'''
aln = alignment.Alignment('\t'.join(['100', '200', '101', '1', '100', '100', '100.00', '300', '300', '1', '1', 'ref', 'qry']))
snp0 = snp.Snp('\t'.join(['140', 'A', 'T', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # snp
snp0 = variant.Variant(snp0)
snp1 = snp.Snp('\t'.join(['140', 'A', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry
snp2 = snp.Snp('\t'.join(['141', 'C', '.', '40', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from qry
del1 = variant.Variant(snp1)
del2 = variant.Variant(snp1)
self.assertTrue(del2.update_indel(snp2))
snp3 = snp.Snp('\t'.join(['150', '.', 'A', '50', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref
snp4 = snp.Snp('\t'.join(['150', '.', 'C', '51', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref
snp5 = snp.Snp('\t'.join(['150', '.', 'G', '52', 'x', 'x', '300', '300', 'x', '1', 'ref', 'qry'])) # del from ref
ins1 = variant.Variant(snp3)
ins2 = variant.Variant(snp3)
self.assertTrue(ins2.update_indel(snp4))
self.assertTrue(ins2.update_indel(snp5))
tests = [
(99, [], (100, False)),
(100, [], (99, False)),
(199, [], (0, False)),
(119, [], (80, False)),
(119, [del1], (80, False)),
(149, [], (50, False)),
(149, [del1], (51, False)),
(149, [del2], (52, False)),
(159, [], (40, False)),
(159, [ins1], (39, False)),
(159, [ins2], (37, False)),
(159, [del1, ins1], (40, False)),
(159, [del1, ins2], (38, False)),
(159, [del2, ins1], (41, False)),
(159, [del2, ins2], (39, False)),
(139, [del1], (39, True)),
(139, [snp0], (60, False)),
(149, [ins1], (49, True)),
]
for ref_coord, variant_list, expected in tests:
got = aln.qry_coords_from_ref_coord(ref_coord, variant_list)
self.assertEqual(expected, got)
# if we reverse the direction of hit in query and reference, should get the same answer
aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start
aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start
got = aln.qry_coords_from_ref_coord(ref_coord, variant_list)
self.assertEqual(expected, got)
aln.qry_start, aln.qry_end = aln.qry_end, aln.qry_start
aln.ref_start, aln.ref_end = aln.ref_end, aln.ref_start
def test_coords_file(self):
'''test coords_file'''
expected = [
'\t'.join(['61', '900', '1', '840', '840', '840', '99.76', '1000', '840', '1', '1', 'test_ref1', 'test_qry1', '[CONTAINS]']),
'\t'.join(['62', '901', '2', '841', '841', '850', '99.66', '999', '839', '1', '1', 'test_ref2', 'test_qry2', '[CONTAINS]']),
'\t'.join(['63', '902', '3', '842', '842', '860', '99.56', '998', '838', '1', '1', 'test_ref3', 'test_qry3', '[CONTAINS]'])
]
expected = [alignment.Alignment(x) for x in expected]
infiles = [os.path.join(data_dir, 'coords_file_test_with_header.coords'), os.path.join(data_dir, 'coords_file_test_no_header.coords')]
for fname in infiles:
fr = coords_file.reader(fname)
alignments = [x for x in fr]
self.assertEqual(alignments, expected)
def test_init_nucmer(self):
'''test __init__ nucmer'''
line = '\t'.join(['1', '100', '2', '200', '101', '202', '42.42', '123', '456', '-1', '0', 'ref', 'qry', '[FOO]'])
a = alignment.Alignment(line)
self.assertEqual(a.ref_start, 0)
self.assertEqual(a.ref_end, 99)
self.assertEqual(a.qry_start, 1)
self.assertEqual(a.qry_end, 199)
self.assertEqual(a.hit_length_ref, 101)
self.assertEqual(a.hit_length_qry, 202)
self.assertEqual(a.percent_identity, 42.42)
self.assertEqual(a.ref_length, 123)
self.assertEqual(a.qry_length, 456)
self.assertEqual(a.frame, -1)
self.assertEqual(a.ref_name, 'ref')
self.assertEqual(a.qry_name, 'qry')
def test_init_promer(self):
'''test __init__ promer'''
line = '\t'.join(['1', '1398', '4891054', '4892445', '1398', '1392', '89.55', '93.18', '0.21', '1398', '5349013', '1', '1', 'ref', 'qry', '[CONTAINED]'])
a = alignment.Alignment(line)
self.assertEqual(a.ref_start, 0)
self.assertEqual(a.ref_end, 1397)
self.assertEqual(a.qry_start, 4891053)
self.assertEqual(a.qry_end, 4892444)
self.assertEqual(a.hit_length_ref, 1398)
self.assertEqual(a.hit_length_qry, 1392)
self.assertEqual(a.percent_identity, 89.55)
self.assertEqual(a.ref_length, 1398)
self.assertEqual(a.qry_length, 5349013)
self.assertEqual(a.frame, 1)
self.assertEqual(a.ref_name, 'ref')
self.assertEqual(a.qry_name, 'qry')
def test_contig_overlap_trimmer(self):
'''Test contig overlap trimming'''
# test data
test_fasta_file = os.path.join(data_dir, "TRIMMING_input_1.fa")
test_overlap_coords = ['\t'.join(['1', '4', '57', '60', '4', '4', '100.00', '60', '60', '1', '1', 'contig1', 'contig1']),
'\t'.join(['1', '4', '57', '60', '4', '4', '100.00', '60', '60', '1', '1', 'contig2', 'contig2']),
'\t'.join(['2', '4', '57', '59', '3', '3', '100.00', '60', '60', '1', '1', 'contig3', 'contig3']),
'\t'.join(['2', '4', '54', '56', '3', '3', '100.00', '60', '60', '1', '1', 'contig4', 'contig4']),
'\t'.join(['1', '3', '58', '60', '3', '3', '100.00', '60', '60', '1', '1', 'contig4', 'contig4']),
'\t'.join(['1', '4', '57', '60', '4', '4', '100.00', '60', '60', '1', '1', 'contig5', 'contig5']),
'\t'.join(['1', '2', '59', '60', '2', '2', '100.00', '60', '60', '1', '1', 'contig6', 'contig6']), #Overlap too short
'\t'.join(['1', '12', '49', '60', '12', '12', '100.00', '60', '60', '1', '1', 'contig7', 'contig7']), # Trimmed length would be too short
'\t'.join(['1', '3', '60', '58', '3', '3', '100.00', '60', '60', '-1', '-1', 'contig8', 'contig8']), #overlap reversed
# No overlap for contig 9
'\t'.join(['4', '7', '36', '38', '4', '4', '100.00', '60', '60', '1', '-1', 'contig10', 'contig10']), #beyond offset
]
test_overlap_alignments = [alignment.Alignment(coord) for coord in test_overlap_coords]
overlap_trimmer = contig_overlap_trimmer.ContigOverlapTrimmer(fasta_file = test_fasta_file,
alignments = test_overlap_alignments,
overlap_offset = 10,
overlap_min_length=3,
overlap_max_length=12,
)
overlap_trimmer.run()
self.assertTrue(os.path.isfile(overlap_trimmer.output_file))
self.assertTrue(os.path.isfile(overlap_trimmer.summary_file))
expected_contigs = {}
tasks.file_to_dict(os.path.join(data_dir, "TRIMMING_output_1.fa"), expected_contigs)
for id in expected_contigs.keys():
self.assertTrue(expected_contigs[id] == overlap_trimmer.contigs[id])
os.remove(overlap_trimmer.output_file)
os.remove(overlap_trimmer.summary_file)
