class TestSearchBadMAF(unittest.TestCase):
"""Test index searching on an incorrectly-formatted MAF."""
def setUp(self):
self.idx = MafIndex("MAF/ucsc_mm9_chr10_bad.mafindex",
"MAF/ucsc_mm9_chr10_bad.maf", "mm9.chr10")
self.assertEqual(len(self.idx), 48)
def test_incorrect_bundle_coords(self):
search = self.idx.search((3013219, ), (3013319, ))
self.assertRaises(ValueError, next, search)
class TestSearchBadMAF(unittest.TestCase):
"""Test index searching on an incorrectly-formatted MAF"""
def setUp(self):
self.idx = MafIndex("MAF/ucsc_mm9_chr10_bad.mafindex",
"MAF/ucsc_mm9_chr10_bad.maf", "mm9.chr10")
self.assertEqual(len(self.idx), 48)
def test_incorrect_bundle_coords(self):
search = self.idx.search((3013219,), (3013319,))
self.assertRaises(ValueError, next, search)
class TestSearchGoodMAF(unittest.TestCase):
"""Test index searching on a properly-formatted MAF."""
def setUp(self):
self.idx = MafIndex("MAF/ucsc_mm9_chr10.mafindex",
"MAF/ucsc_mm9_chr10.maf", "mm9.chr10")
self.assertEqual(len(self.idx), 48)
def test_invalid_type_1(self):
search = self.idx.search((500, 1000), ("string", 1500))
self.assertRaises(TypeError, next, search)
def test_invalid_type_2(self):
search = self.idx.search((500, 1000), (750, 1500.25))
self.assertRaises(TypeError, next, search)
def test_invalid_exon_count(self):
search = self.idx.search((0, 1000, 2000), (500, 1500))
self.assertRaises(ValueError, next, search)
def test_invalid_exon_schema(self):
search = self.idx.search((0, 1000, 2000), (250, 500, 2500))
self.assertRaises(ValueError, next, search)
def test_correct_retrieval_1(self):
"""Correct retrieval of Cnksr3 in mouse."""
search = self.idx.search((3014742, 3018161), (3015028, 3018644))
results = list(search)
self.assertEqual(len(results), 4 + 4)
self.assertEqual({len(x)
for x in results}, {4, 1, 9, 10, 4, 3, 5, 1})
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
self.assertEqual(
{x.annotations["start"]
for y in results for x in y}, {
3014742, 6283, 184202, 1257, 3014778, 3014795, 184257,
6365, 15871286, 16389854, 16169492, 171521, 7816, 1309,
3014842, 1371, 7842, 171548, 16169512, 16389874, 15871306,
6404, 184317, 14750994, 3018161, 16390178, 15871611,
16169818, 3018230, 15871676, 16390243, 3018359, 16390338,
15871771, 184712, 16169976, 3018482
})
def test_correct_retrieval_2(self):
search = self.idx.search((3009319, 3021421), (3012566, 3021536))
results = list(search)
self.assertEqual(len(results), 6)
self.assertEqual({len(x) for x in results}, {2, 4, 5, 14, 7, 6})
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
self.assertEqual(
{x.annotations["start"]
for y in results for x in y}, {
3009319, 11087, 3012076, 16160203, 16379004, 15860456,
3012441, 15860899, 16379447, 16160646, 180525, 3021421,
9910, 996, 16173434, 16393782, 15875216, 11047, 175213,
3552, 677, 78072203, 3590, 95587, 14757054, 3021465, 9957,
16173483, 16393831, 15875265, 78072243, 14757099, 3021494,
16173516, 16393864, 15875298, 78072287, 14757144
})
def test_correct_retrieval_3(self):
"""Following issue 1083.
https://github.com/biopython/biopython/issues/1083
"""
search = self.idx.search((3012076, 3012076 + 300),
(3012076 + 100, 3012076 + 400))
results = list(search)
self.assertEqual(len(results), 2)
self.assertEqual({len(x) for x in results}, {4, 5})
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
self.assertEqual(
{x.annotations["start"]
for y in results for x in y}, {
3012076, 16160203, 16379004, 15860456, 3012441, 15860899,
16379447, 16160646, 180525
})
def test_correct_block_boundary(self):
"""Following issues 504 and 1086.
https://github.com/biopython/biopython/pull/504
https://github.com/biopython/biopython/pull/1086#issuecomment-285080702
We test what happens at the boundary between these two MAF blocks:
a score=19159.000000
s mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG
s hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
i hg18.chr6 I 9085 C 0
s panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
q panTro2.chr6 99999999999999999999999-9999999999999999999-9999
i panTro2.chr6 I 9106 C 0
s calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT
i calJac1.Contig6394 N 0 C 0
s loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC
q loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997
i loxAfr1.scaffold_75566 N 0 C 0
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
# Segments ending at the end of the first block
search = self.idx.search([3014687], [3014689])
self.assertEqual(len(list(search)), 1)
search = self.idx.search([3014688], [3014689])
self.assertEqual(len(list(search)), 1)
# Segments starting at the beginning of the second block
search = self.idx.search([3014689], [3014690])
self.assertEqual(len(list(search)), 1)
search = self.idx.search([3014689], [3014691])
self.assertEqual(len(list(search)), 1)
# Segments overlapping the 2 blocks
search = self.idx.search([3014688], [3014690])
self.assertEqual(len(list(search)), 2)
search = self.idx.search([3014687], [3014690])
self.assertEqual(len(list(search)), 2)
search = self.idx.search([3014687], [3014691])
self.assertEqual(len(list(search)), 2)
def test_correct_block_length(self):
"""Following issues 504 and 1086.
https://github.com/biopython/biopython/pull/504
https://github.com/biopython/biopython/pull/1086#issuecomment-285080702
We get the alignement corresponding to the following whole MAF block
and check that the lengths of its sequences are correct:
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014689], [3014689 + 53])
seq_dict = {seqrec.id: seqrec.seq for seqrec in ali}
correct_lengths = {
"mm9.chr10": 53,
"hg18.chr6": 53,
"panTro2.chr6": 53,
"calJac1.Contig6394": 53,
"otoGar1.scaffold_334.1-359464": 52,
"loxAfr1.scaffold_75566": 54
}
for seq_id, length in correct_lengths.items():
self.assertEqual(len(seq_dict[seq_id].ungap("-")), length)
def test_correct_spliced_sequences_1(self):
"""Checking that spliced sequences are correct.
We get the alignement corresponding to the following whole MAF block
and check that the sequences are correct:
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014689], [3014689 + 53])
seq_dict = {seqrec.id: seqrec.seq for seqrec in ali}
correct_sequences = {
"mm9.chr10":
"GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG",
"hg18.chr6":
"GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"panTro2.chr6":
"GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"calJac1.Contig6394":
"GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG",
"otoGar1.scaffold_334.1-359464":
"GGAAGCATAAACTTTTAATCTATGAAATATCAAATCACTTGGGCAATAGCTG",
"loxAfr1.scaffold_75566":
"GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG"
}
for seq_id, sequence in correct_sequences.items():
self.assertEqual(seq_dict[seq_id].ungap("-"), sequence)
def test_correct_spliced_sequences_2(self):
"""Checking that spliced sequences are correct.
We get spliced alignements from following MAF blocks
and check that the sequences are correct:
a score=19159.000000
s mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG
s hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
i hg18.chr6 I 9085 C 0
s panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
q panTro2.chr6 99999999999999999999999-9999999999999999999-9999
i panTro2.chr6 I 9106 C 0
s calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT
i calJac1.Contig6394 N 0 C 0
s loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC
q loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997
i loxAfr1.scaffold_75566 N 0 C 0
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014644, 3014689],
[3014644 + 45, 3014689 + 53])
seq_dict = {seqrec.id: seqrec.seq for seqrec in ali}
correct_sequences = {
"mm9.chr10":
"CCTGTACCCTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTGGGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG",
"hg18.chr6":
"CCTATACCTTTCTTTTATGAGAATTTTGTTTTAATCCTAAACTTTTGGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"panTro2.chr6":
"CCTATACCTTTCTTTTATGAGAATTTTGTTTTAATCCTAAACTTTTGGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"calJac1.Contig6394":
"CCTATACCTTTCTTTCATGAGAATTTTGTTTGAATCCTAAACTTTTGGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG",
"otoGar1.scaffold_334.1-359464":
"GGAAGCATAAACTTTTAATCTATGAAATATCAAATCACTTGGGCAATAGCTG",
"loxAfr1.scaffold_75566":
"TTTGGTTAGAATTATGCTTTAATTCAAAACTTCCGGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG"
}
for seq_id, sequence in correct_sequences.items():
self.assertEqual(seq_dict[seq_id].ungap("-"), sequence)
class TestSearchGoodMAF(unittest.TestCase):
"""Test index searching on a properly-formatted MAF"""
def setUp(self):
self.idx = MafIndex("MAF/ucsc_mm9_chr10.mafindex",
"MAF/ucsc_mm9_chr10.maf", "mm9.chr10")
self.assertEqual(len(self.idx), 48)
def test_invalid_type_1(self):
search = self.idx.search((500, 1000), ("string", 1500))
self.assertRaises(TypeError, next, search)
def test_invalid_type_2(self):
search = self.idx.search((500, 1000), (750, 1500.25))
self.assertRaises(TypeError, next, search)
def test_invalid_exon_count(self):
search = self.idx.search((0, 1000, 2000), (500, 1500))
self.assertRaises(ValueError, next, search)
def test_invalid_exon_schema(self):
search = self.idx.search((0, 1000, 2000), (250, 500, 2500))
self.assertRaises(ValueError, next, search)
def test_correct_retrieval_1(self):
search = self.idx.search((3014742, 3018161), (3015028, 3018644))
results = [x for x in search]
self.assertEqual(len(results), 12)
self.assertEqual(set([len(x) for x in results]),
set([5, 10, 7, 6, 3, 1, 1, 1, 2, 4, 4, 9]))
self.assertEqual(set([x.annotations["start"] for y in results
for x in y]),
set([3018359, 16390338, 15871771, 184712,
16169512, 16169976, 3014842, 1371, 7842,
171548, 16389874, 15871306, 6404, 184317,
14750994, 3015028, 1616, 8040, 171763,
16169731, 6627, 184539, 3014689, 15870832,
16389401, 6228, 184148, 1201, 3018230,
15871676, 16390243, 3014778, 3018482, 3017743,
3018644, 78070420, 3014742, 6283, 184202,
1257, 3018161, 16390178, 15871611, 16169818,
3014795, 184257, 6365, 15871286, 16389854,
16169492, 171521, 7816, 1309]))
def test_correct_retrieval_2(self):
search = self.idx.search((3009319, 3021421), (3012566, 3021536))
results = [x for x in search]
self.assertEqual(len(results), 8)
self.assertEqual(set([len(x) for x in results]),
set([14, 5, 2, 6, 7, 15, 6, 4]))
self.assertEqual(set([x.annotations["start"] for y in results
for x in y]),
set([3021421, 9910, 996, 16173434, 16393782,
15875216, 11047, 175213, 3552, 677, 78072203,
3590, 95587, 14757054, 3012441, 15860899,
16379447, 16160646, 180525, 3009319, 11087,
3012566, 15861013, 16379561, 16160760, 180626,
310, 3021465, 9957, 16173483, 16393831,
15875265, 78072243, 14757099, 3021275, 9741,
838, 16173265, 16393613, 15875047, 10878,
175057, 3382, 521, 78072035, 73556, 3422,
95418, 14756885, 3021494, 16173516, 16393864,
15875298, 78072287, 14757144, 3012076,
16160203, 16379004, 15860456]))
def test_correct_retrieval_3(self):
search = self.idx.search((3012076, 3012076 + 300), (3012076 + 100, 3012076 + 400))
results = [x for x in search]
self.assertEqual(len(results), 2)
self.assertEqual(set([len(x) for x in results]),
set([4, 5]))
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
self.assertEqual(
set([x.annotations["start"] for y in results for x in y]),
set([
3012076, 16160203, 16379004, 15860456,
3012441, 15860899, 16379447, 16160646, 180525]))
class TestSearchGoodMAF(unittest.TestCase):
"""Test index searching on a properly-formatted MAF."""
def setUp(self):
self.idx = MafIndex("MAF/ucsc_mm9_chr10.mafindex",
"MAF/ucsc_mm9_chr10.maf", "mm9.chr10")
self.assertEqual(len(self.idx), 48)
def test_invalid_type_1(self):
search = self.idx.search((500, 1000), ("string", 1500))
self.assertRaises(TypeError, next, search)
def test_invalid_type_2(self):
search = self.idx.search((500, 1000), (750, 1500.25))
self.assertRaises(TypeError, next, search)
def test_invalid_exon_count(self):
search = self.idx.search((0, 1000, 2000), (500, 1500))
self.assertRaises(ValueError, next, search)
def test_invalid_exon_schema(self):
search = self.idx.search((0, 1000, 2000), (250, 500, 2500))
self.assertRaises(ValueError, next, search)
def test_correct_retrieval_1(self):
"""Correct retrieval of Cnksr3 in mouse."""
search = self.idx.search((3014742, 3018161), (3015028, 3018644))
results = [x for x in search]
self.assertEqual(len(results), 4 + 4)
self.assertEqual(set([len(x) for x in results]),
set([4, 1, 9, 10, 4, 3, 5, 1]))
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
self.assertEqual(
set([x.annotations["start"] for y in results for x in y]),
set([
3014742, 6283, 184202, 1257,
3014778,
3014795, 184257, 6365, 15871286, 16389854, 16169492, 171521, 7816, 1309,
3014842, 1371, 7842, 171548, 16169512, 16389874, 15871306, 6404, 184317, 14750994,
3018161, 16390178, 15871611, 16169818,
3018230, 15871676, 16390243,
3018359, 16390338, 15871771, 184712, 16169976, 3018482]))
def test_correct_retrieval_2(self):
search = self.idx.search((3009319, 3021421), (3012566, 3021536))
results = [x for x in search]
self.assertEqual(len(results), 6)
self.assertEqual(set([len(x) for x in results]),
set([2, 4, 5, 14, 7, 6]))
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
self.assertEqual(
set([x.annotations["start"] for y in results for x in y]),
set([
3009319, 11087,
3012076, 16160203, 16379004, 15860456,
3012441, 15860899, 16379447, 16160646, 180525,
3021421, 9910, 996, 16173434, 16393782, 15875216, 11047, 175213, 3552, 677, 78072203, 3590, 95587, 14757054,
3021465, 9957, 16173483, 16393831, 15875265, 78072243, 14757099,
3021494, 16173516, 16393864, 15875298, 78072287, 14757144]))
def test_correct_retrieval_3(self):
"""Following issue 1083.
https://github.com/biopython/biopython/issues/1083
"""
search = self.idx.search((3012076, 3012076 + 300), (3012076 + 100, 3012076 + 400))
results = [x for x in search]
self.assertEqual(len(results), 2)
self.assertEqual(set([len(x) for x in results]),
set([4, 5]))
# Code formatting note:
# Expected start coordinates are grouped by alignment blocks
self.assertEqual(
set([x.annotations["start"] for y in results for x in y]),
set([
3012076, 16160203, 16379004, 15860456,
3012441, 15860899, 16379447, 16160646, 180525]))
def test_correct_block_boundary(self):
"""Following issues 504 and 1086.
https://github.com/biopython/biopython/pull/504
https://github.com/biopython/biopython/pull/1086#issuecomment-285080702
We test what happens at the boundary between these two MAF blocks:
a score=19159.000000
s mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG
s hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
i hg18.chr6 I 9085 C 0
s panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
q panTro2.chr6 99999999999999999999999-9999999999999999999-9999
i panTro2.chr6 I 9106 C 0
s calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT
i calJac1.Contig6394 N 0 C 0
s loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC
q loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997
i loxAfr1.scaffold_75566 N 0 C 0
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
# Segments ending at the end of the first block
search = self.idx.search([3014687], [3014689])
self.assertEqual(len(list(search)), 1)
search = self.idx.search([3014688], [3014689])
self.assertEqual(len(list(search)), 1)
# Segments starting at the beginning of the second block
search = self.idx.search([3014689], [3014690])
self.assertEqual(len(list(search)), 1)
search = self.idx.search([3014689], [3014691])
self.assertEqual(len(list(search)), 1)
# Segments overlapping the 2 blocks
search = self.idx.search([3014688], [3014690])
self.assertEqual(len(list(search)), 2)
search = self.idx.search([3014687], [3014690])
self.assertEqual(len(list(search)), 2)
search = self.idx.search([3014687], [3014691])
self.assertEqual(len(list(search)), 2)
def test_correct_block_length(self):
"""Following issues 504 and 1086.
https://github.com/biopython/biopython/pull/504
https://github.com/biopython/biopython/pull/1086#issuecomment-285080702
We get the alignement corresponding to the following whole MAF block
and check that the lengths of its sequences are correct:
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014689], [3014689 + 53])
seq_dict = dict([(seqrec.id, seqrec.seq) for seqrec in ali])
correct_lengths = {
"mm9.chr10": 53,
"hg18.chr6": 53,
"panTro2.chr6": 53,
"calJac1.Contig6394": 53,
"otoGar1.scaffold_334.1-359464": 52,
"loxAfr1.scaffold_75566": 54}
for seq_id, length in correct_lengths.items():
self.assertEqual(len(seq_dict[seq_id].ungap('-')), length)
def test_correct_spliced_sequences_1(self):
"""Checking that spliced sequences are correct.
We get the alignement corresponding to the following whole MAF block
and check that the sequences are correct:
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014689], [3014689 + 53])
seq_dict = dict([(seqrec.id, seqrec.seq) for seqrec in ali])
correct_sequences = {
"mm9.chr10": "GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG",
"hg18.chr6": "GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"panTro2.chr6": "GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"calJac1.Contig6394": "GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG",
"otoGar1.scaffold_334.1-359464": "GGAAGCATAAACTTTTAATCTATGAAATATCAAATCACTTGGGCAATAGCTG",
"loxAfr1.scaffold_75566": "GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG"}
for seq_id, sequence in correct_sequences.items():
self.assertEqual(seq_dict[seq_id].ungap('-'), sequence)
def test_correct_spliced_sequences_2(self):
"""Checking that spliced sequences are correct.
We get spliced alignements from following MAF blocks
and check that the sequences are correct:
a score=19159.000000
s mm9.chr10 3014644 45 + 129993255 CCTGTACC---CTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTG
s hg18.chr6 15870786 46 - 170899992 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
i hg18.chr6 I 9085 C 0
s panTro2.chr6 16389355 46 - 173908612 CCTATACCTTTCTTTTATGAGAA-TTTTGTTTTAATCCTAAAC-TTTT
q panTro2.chr6 99999999999999999999999-9999999999999999999-9999
i panTro2.chr6 I 9106 C 0
s calJac1.Contig6394 6182 46 + 133105 CCTATACCTTTCTTTCATGAGAA-TTTTGTTTGAATCCTAAAC-TTTT
i calJac1.Contig6394 N 0 C 0
s loxAfr1.scaffold_75566 1167 34 - 10574 ------------TTTGGTTAGAA-TTATGCTTTAATTCAAAAC-TTCC
q loxAfr1.scaffold_75566 ------------99999699899-9999999999999869998-9997
i loxAfr1.scaffold_75566 N 0 C 0
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e otoGar1.scaffold_334.1-359464 181217 2931 - 359464 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
a score=40840.000000
s mm9.chr10 3014689 53 + 129993255 GGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCT-TTGGAAAGAGTTG
s hg18.chr6 15870832 53 - 170899992 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
i hg18.chr6 C 0 I 401
s panTro2.chr6 16389401 53 - 173908612 GGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTT-TGGGAAATAGTGG
q panTro2.chr6 9999999999999999999999999999999999999999-9999999999999
i panTro2.chr6 C 0 I 400
s calJac1.Contig6394 6228 53 + 133105 GGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTT-TGGGAAACAGTGG
i calJac1.Contig6394 C 0 I 2
s otoGar1.scaffold_334.1-359464 184148 52 - 359464 GGAAGCATAAACT-TTTAATCTATGAAATATCAAATCACT-TGGGCAATAGCTG
q otoGar1.scaffold_334.1-359464 7455455669566-99665699769895555689997599-9984787795599
i otoGar1.scaffold_334.1-359464 I 2931 I 2
s loxAfr1.scaffold_75566 1201 54 - 10574 GGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG
q loxAfr1.scaffold_75566 899989799999979999999999999999797999999999999999999999
i loxAfr1.scaffold_75566 C 0 I 2
e tupBel1.scaffold_114895.1-498454 167376 4145 - 498454 I
e echTel1.scaffold_288249 87661 7564 + 100002 I
e ponAbe2.chr6 16161448 8044 - 174210431 I
"""
ali = self.idx.get_spliced([3014644, 3014689], [3014644 + 45, 3014689 + 53])
seq_dict = dict([(seqrec.id, seqrec.seq) for seqrec in ali])
correct_sequences = {
"mm9.chr10": "CCTGTACCCTTTGGTGAGAATTTTTGTTTCAGTGTTAAAAGTTTGGGGAGCATAAAACTCTAAATCTGCTAAATGTCTTGTCCCTTTGGAAAGAGTTG",
"hg18.chr6": "CCTATACCTTTCTTTTATGAGAATTTTGTTTTAATCCTAAACTTTTGGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"panTro2.chr6": "CCTATACCTTTCTTTTATGAGAATTTTGTTTTAATCCTAAACTTTTGGGATCATAAACCATTTAATCTGTGAAATATCTAATCTTTTGGGAAATAGTGG",
"calJac1.Contig6394": "CCTATACCTTTCTTTCATGAGAATTTTGTTTGAATCCTAAACTTTTGGGATCATAAGCCATTTAATCTGTGAAATGTGAAATCTTTTGGGAAACAGTGG",
"otoGar1.scaffold_334.1-359464": "GGAAGCATAAACTTTTAATCTATGAAATATCAAATCACTTGGGCAATAGCTG",
"loxAfr1.scaffold_75566": "TTTGGTTAGAATTATGCTTTAATTCAAAACTTCCGGGAGTATAAACCATTTAGTCTGCGAAATGCCAAATCTTCAGGGGAAAAAGCTG"}
for seq_id, sequence in correct_sequences.items():
self.assertEqual(seq_dict[seq_id].ungap('-'), sequence)