def setUp(self):
self.idx = MafIndex(
"MAF/ucsc_mm9_chr10_big.mafindex",
"MAF/ucsc_mm9_chr10_big.maf",
"mm9.chr10",
)
self.assertEqual(len(self.idx), 983)
def main():
parser = argparse.ArgumentParser(description='report pair-wise PID in intervals',
prog='maf2pid')
parser.add_argument('--splst', dest='splst', help='species list')
parser.add_argument('--bed', dest='interval', help='bed intervals')
parser.add_argument('--output', dest='output', help='output file')
if len(sys.argv) < 4:
parser.print_help()
sys.exit(1)
args = parser.parse_args()
intervals_by_chrom = parse_bed(args.interval)
[species, pairwise] = make_pair_names(args.splst)
fout = open(args.output, 'w')
header = "#chrom\tstart\tend\tpme"
for i in pairwise :
header += "\t"+i
fout.write( header + "\n")
for chrom in intervals_by_chrom.keys() :
sqlite_file = chrom + ".mafindex"
maf_file = chrom + ".7sp.maf"
target_seqname = "hg19." + chrom
idx = MafIndex(sqlite_file, maf_file, target_seqname)
# MafIndex.get_spliced(starts, ends, strand='+1')
starts = intervals_by_chrom[chrom][0]
ends = intervals_by_chrom[chrom][1]
names = intervals_by_chrom[chrom][2]
for k in range(len(starts)) :
result = idx.get_spliced([starts[k]], [ends[k]], strand='+1')
recsp = [rec.id.split(".")[0] for rec in result]
PIDscores = {}
for i in range(len(recsp)-1) :
for j in range(i+1, len(recsp)) :
pw = recsp[i]+ "_"+ recsp[j]
if pw not in pairwise :
pw = recsp[j]+ "_"+ recsp[i]
if (pw in pairwise) and (not PIDscores.has_key(pw)): # exclude paralogs
pid = get_PID(str(result[i].seq), str(result[j].seq))
PIDscores[pw] = pid
for pw in pairwise :
if pw not in PIDscores :
PIDscores[pw] = -1
fout.write(chrom + "\t" + str(starts[k]) + "\t" + str(ends[k]) + "\tpme_" + names[k])
for pw in pairwise :
fout.write("\t"+ "{:.5f}".format(PIDscores[pw]))
fout.write("\n")
fout.close()
return
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 TestSpliceGoodMAF(unittest.TestCase):
"""Test in silico splicing on a correctly-formatted MAF"""
def setUp(self):
self.idx = MafIndex("MAF/ucsc_mm9_chr10_big.mafindex",
"MAF/ucsc_mm9_chr10_big.maf", "mm9.chr10")
self.assertEqual(len(self.idx), 983)
def test_invalid_strand(self):
self.assertRaises(ValueError,
self.idx.get_spliced,
(0, 1000), (500, 1500), ".")
def test_no_alignment(self):
result = self.idx.get_spliced((0, 1000), (500, 1500), 1)
self.assertEqual(len(result), 1)
self.assertEqual(len(result[0].seq), 1000)
self.assertEqual(str(result[0].seq), "N" * 1000)
def test_correct_retrieval_1(self):
"""Correct retrieval of Cnksr3 in mouse.
This is the real thing. We're pulling the spliced alignment of
an actual gene (Cnksr3) in mouse. It should perfectly match the
spliced transcript pulled independently from UCSC.
"""
result = self.idx.get_spliced((3134303, 3185733, 3192055, 3193589,
3203538, 3206102, 3208126, 3211424,
3211872, 3217393, 3219697, 3220356,
3225954),
(3134909, 3185897, 3192258, 3193677,
3203580, 3206222, 3208186, 3211493,
3212019, 3217518, 3219906, 3220446,
3227479), 1)
cnksr3 = str(SeqIO.read("MAF/cnksr3.fa", "fasta").seq).upper()
mm9_seq = "".join([str(x.seq) for x in result
if x.id.startswith("mm9")]).replace("-", "")
self.assertEqual(mm9_seq, cnksr3)
def test_ucscbin(self):
data = [(25079603, 25079787, 776), (25128173, 25128248, 776),
(50312474, 50312703, 968), (41905591, 41906101, 904),
(16670899, 16673060, 712), (75495356, 75495494, 1160),
(92259501, 92261053, 1288), (83834063, 83838132, 1224),
(7309597, 7310411, 640), (6190410, 6190999, 632)]
for x, y, z in data:
self.assertEqual(MafIndex._ucscbin(x, y), z)
for x, y, z in data:
self.assertRaises(TypeError, MafIndex._ucscbin, str(x), str(y))
def test_region2bin(self):
data = [(25079603, 25079787, set([0, 1, 11, 96, 776])),
(25128173, 25128248, set([0, 1, 11, 96, 776])),
(50312474, 50312703, set([0, 1, 968, 14, 120])),
(41905591, 41906101, set([0, 1, 904, 13, 112])),
(16670899, 16673060, set([0, 1, 10, 712, 88])),
(75495356, 75495494, set([0, 1, 2, 1160, 144, 17])),
(92259501, 92261053, set([0, 1, 2, 1288, 160, 19])),
(83834063, 83838132, set([0, 1, 2, 1224, 18, 152])),
(7309597, 7310411, set([0, 1, 640, 79, 9])),
(6190410, 6190999, set([0, 1, 632, 78, 9]))]
for x, y, z in data:
self.assertEqual(MafIndex._region2bin(x, y), z)
for x, y, z in data:
self.assertRaises(TypeError, MafIndex._region2bin, str(x), str(y))
def test_region2bin(self):
data = [(25079603, 25079787, {0, 1, 11, 96, 776}),
(25128173, 25128248, {0, 1, 11, 96, 776}),
(50312474, 50312703, {0, 1, 968, 14, 120}),
(41905591, 41906101, {0, 1, 904, 13, 112}),
(16670899, 16673060, {0, 1, 10, 712, 88}),
(75495356, 75495494, {0, 1, 2, 1160, 144, 17}),
(92259501, 92261053, {0, 1, 2, 1288, 160, 19}),
(83834063, 83838132, {0, 1, 2, 1224, 18, 152}),
(7309597, 7310411, {0, 1, 640, 79, 9}),
(6190410, 6190999, {0, 1, 632, 78, 9})]
for x, y, z in data:
self.assertEqual(MafIndex._region2bin(x, y), z)
for x, y, z in data:
self.assertRaises(TypeError, MafIndex._region2bin, str(x), str(y))
def test_ucscbin(self):
data = [(25079603, 25079787, 776),
(25128173, 25128248, 776),
(50312474, 50312703, 968),
(41905591, 41906101, 904),
(16670899, 16673060, 712),
(75495356, 75495494, 1160),
(92259501, 92261053, 1288),
(83834063, 83838132, 1224),
(7309597, 7310411, 640),
(6190410, 6190999, 632)]
for x, y, z in data:
self.assertEqual(MafIndex._ucscbin(x, y), z)
for x, y, z in data:
self.assertRaises(TypeError, MafIndex._ucscbin, str(x), str(y))
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)
def test_good_big(self):
idx = MafIndex(self.tmpfile, "MAF/ucsc_mm9_chr10_big.maf",
"mm9.chr10")
self.assertEquals(len(idx), 983)
class TestGetRecord(unittest.TestCase):
"""Make sure we can seek and fetch records properly."""
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_records_begin(self):
recs = {}
recs[0] = SeqRecord(Seq(
"TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAA"
"CACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTA"
"AAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCAT"
"AGAAGATGACATAATGTATTTTCCTTTTGGTT"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={
"start": 3009319,
"srcSize": 129993255,
"strand": 1,
"size": 162
})
recs[1] = SeqRecord(Seq(
"TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGG"
"TTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCA"
"GAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCAT"
"GGAAACTGATGTCAAATACTTTCCCTTTGGTT"),
id="oryCun1.scaffold_133159",
name="oryCun1.scaffold_133159",
description="",
annotations={
"start": 11087,
"srcSize": 13221,
"strand": 1,
"size": 164
})
fetched_recs = self.idx._get_record(34)
for i in range(2):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
def test_records_end(self):
recs = {}
recs[0] = SeqRecord(
Seq("TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={
"start": 3021494,
"srcSize": 129993255,
"strand": 1,
"size": 42
})
recs[1] = SeqRecord(
Seq("TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="ponAbe2.chr6",
name="ponAbe2.chr6",
description="",
annotations={
"start": 16173516,
"srcSize": 174210431,
"strand": -1,
"size": 46
})
recs[2] = SeqRecord(
Seq("TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="panTro2.chr6",
name="panTro2.chr6",
description="",
annotations={
"start": 16393864,
"srcSize": 173908612,
"strand": -1,
"size": 46
})
recs[3] = SeqRecord(
Seq("TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="hg18.chr6",
name="hg18.chr6",
description="",
annotations={
"start": 15875298,
"srcSize": 170899992,
"strand": -1,
"size": 46
})
recs[4] = SeqRecord(
Seq("TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT"),
id="canFam2.chr1",
name="canFam2.chr1",
description="",
annotations={
"start": 78072287,
"srcSize": 125616256,
"strand": -1,
"size": 46
})
recs[5] = SeqRecord(
Seq("TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----"),
id="ornAna1.chr2",
name="ornAna1.chr2",
description="",
annotations={
"start": 14757144,
"srcSize": 54797317,
"strand": -1,
"size": 36
})
fetched_recs = self.idx._get_record(99228)
for i in range(6):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
def test_good_small(self):
idx = MafIndex(self.tmpfile, "MAF/ucsc_mm9_chr10.maf", "mm9.chr10")
self.assertEquals(len(idx), 48)
class TestGetRecord(unittest.TestCase):
"""Make sure we can seek and fetch records properly"""
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_records_begin(self):
recs = {}
recs[0] = SeqRecord(Seq("TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAA"
"CACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTA"
"AAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCAT"
"AGAAGATGACATAATGTATTTTCCTTTTGGTT"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={"start": 3009319,
"srcSize": 129993255,
"strand": 1,
"size": 162})
recs[1] = SeqRecord(Seq("TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGG"
"TTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCA"
"GAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCAT"
"GGAAACTGATGTCAAATACTTTCCCTTTGGTT"),
id="oryCun1.scaffold_133159",
name="oryCun1.scaffold_133159",
description="",
annotations={"start": 11087,
"srcSize": 13221,
"strand": 1,
"size": 164})
fetched_recs = self.idx._get_record(34)
for i in range(2):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
def test_records_end(self):
recs = {}
recs[0] = SeqRecord(Seq("TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={"start": 3021494,
"srcSize": 129993255,
"strand": 1,
"size": 42})
recs[1] = SeqRecord(Seq("TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="ponAbe2.chr6",
name="ponAbe2.chr6",
description="",
annotations={"start": 16173516,
"srcSize": 174210431,
"strand": -1,
"size": 46})
recs[2] = SeqRecord(Seq("TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="panTro2.chr6",
name="panTro2.chr6",
description="",
annotations={"start": 16393864,
"srcSize": 173908612,
"strand": -1,
"size": 46})
recs[3] = SeqRecord(Seq("TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="hg18.chr6",
name="hg18.chr6",
description="",
annotations={"start": 15875298,
"srcSize": 170899992,
"strand": -1,
"size": 46})
recs[4] = SeqRecord(Seq("TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT"),
id="canFam2.chr1",
name="canFam2.chr1",
description="",
annotations={"start": 78072287,
"srcSize": 125616256,
"strand": -1,
"size": 46})
recs[5] = SeqRecord(Seq("TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----"),
id="ornAna1.chr2",
name="ornAna1.chr2",
description="",
annotations={"start": 14757144,
"srcSize": 54797317,
"strand": -1,
"size": 36})
fetched_recs = self.idx._get_record(99228)
for i in range(6):
self.assertTrue(compare_record(recs[i], fetched_recs[i]))
class TestGetRecord(SeqRecordTestBaseClass):
"""Make sure we can seek and fetch records properly."""
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_records_begin(self):
rec1 = SeqRecord(
Seq(
"TCATAGGTATTTATTTTTAAATATGGTTTGCTTTATGGCTAGAA"
"CACACCGATTACTTAAAATAGGATTAACC--CCCATACACTTTA"
"AAAATGATTAAACAACATTTCTGCTGCTCGCTCACATTCTTCAT"
"AGAAGATGACATAATGTATTTTCCTTTTGGTT"
),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={
"start": 3009319,
"srcSize": 129993255,
"strand": 1,
"size": 162,
},
)
rec2 = SeqRecord(
Seq(
"TCACAGATATTTACTATTAAATATGGTTTGTTATATGGTTACGG"
"TTCATAGGTTACTTGGAATTGGATTAACCTTCTTATTCATTGCA"
"GAATTGGTTACACTGTGTTCTTGACCTTTGCTTGTTTTCTCCAT"
"GGAAACTGATGTCAAATACTTTCCCTTTGGTT"
),
id="oryCun1.scaffold_133159",
name="oryCun1.scaffold_133159",
description="",
annotations={
"start": 11087,
"srcSize": 13221,
"strand": 1,
"size": 164,
},
)
recs = [rec1, rec2]
fetched_recs = self.idx._get_record(34)
self.compare_records(recs, fetched_recs)
def test_records_end(self):
rec1 = SeqRecord(
Seq("TGTTTAGTACC----ATGCTTAGGAATGATAAACTCACTTAGTGtt"),
id="mm9.chr10",
name="mm9.chr10",
description="",
annotations={
"start": 3021494,
"srcSize": 129993255,
"strand": 1,
"size": 42,
},
)
rec2 = SeqRecord(
Seq("TGTTGCATGTCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="ponAbe2.chr6",
name="ponAbe2.chr6",
description="",
annotations={
"start": 16173516,
"srcSize": 174210431,
"strand": -1,
"size": 46,
},
)
rec3 = SeqRecord(
Seq("TGTTGCATATCCTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="panTro2.chr6",
name="panTro2.chr6",
description="",
annotations={
"start": 16393864,
"srcSize": 173908612,
"strand": -1,
"size": 46,
},
)
rec4 = SeqRecord(
Seq("TGTTGCATGTCGTTTATTCTTTGGCGTGATAGGCTCACCCAATCTT"),
id="hg18.chr6",
name="hg18.chr6",
description="",
annotations={
"start": 15875298,
"srcSize": 170899992,
"strand": -1,
"size": 46,
},
)
rec5 = SeqRecord(
Seq("TGTTAAGTCTCACTTGCTGTTCAAAGTGATAGCTTCACTCCATCAT"),
id="canFam2.chr1",
name="canFam2.chr1",
description="",
annotations={
"start": 78072287,
"srcSize": 125616256,
"strand": -1,
"size": 46,
},
)
rec6 = SeqRecord(
Seq("TGTTTAAAATG----ATTGCTAGAACTTCTA--CTCACTGGA----"),
id="ornAna1.chr2",
name="ornAna1.chr2",
description="",
annotations={
"start": 14757144,
"srcSize": 54797317,
"strand": -1,
"size": 36,
},
)
recs = [rec1, rec2, rec3, rec4, rec5, rec6]
fetched_recs = self.idx._get_record(99228)
self.compare_records(recs, fetched_recs)
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]))
def setUp(self):
self.idx = MafIndex("MAF/ucsc_mm9_chr10_big.mafindex",
"MAF/ucsc_mm9_chr10_big.maf", "mm9.chr10")
self.assertEqual(len(self.idx), 983)
#"fr2": "Fugu",
#"ornAna1": "Platypus",
#"danRer5": "Zebrafish",
#"galGal3": "Chicken",
#"gasAcu1": "Stickleback",
#"xenTro2": "Frog",
#"anoCar1": "Lizard",
#"tetNig1": "Tetraodon",
#"oryLat1": "Medaka"
}
for i, rg in enumerate(bed):
print(str(i+1)+"/"+str(num)+":\t"+rg.name+"\t"+rg.toString())
try:
idx = MafIndex(os.path.join(args.mafdir, rg.chrom+".mafindex"),
os.path.join(args.mafdir, rg.chrom+".maf"),
args.organism+"."+rg.chrom)
except:
print("Generating index file...")
os.remove(os.path.join(args.mafdir, rg.chrom+".mafindex"))
idx = MafIndex(os.path.join(args.mafdir, rg.chrom+".mafindex"),
os.path.join(args.mafdir, rg.chrom+".maf"),
args.organism+"."+rg.chrom)
exon_s = []
exon_e = []
if rg.data:
data = rg.data.split("\t")
if len(data) == 7 and int(data[4]) > 1:
z = rg.extract_blocks()
for g in z:
exon_s.append(g.initial)
#"fr2": "Fugu",
#"ornAna1": "Platypus",
#"danRer5": "Zebrafish",
#"galGal3": "Chicken",
#"gasAcu1": "Stickleback",
#"xenTro2": "Frog",
#"anoCar1": "Lizard",
#"tetNig1": "Tetraodon",
#"oryLat1": "Medaka"
}
for i, rg in enumerate(bed):
print(str(i + 1) + "/" + str(num) + ":\t" + rg.name + "\t" + rg.toString())
try:
idx = MafIndex(os.path.join(args.mafdir, rg.chrom + ".mafindex"),
os.path.join(args.mafdir, rg.chrom + ".maf"),
args.organism + "." + rg.chrom)
except:
print("Generating index file...")
os.remove(os.path.join(args.mafdir, rg.chrom + ".mafindex"))
idx = MafIndex(os.path.join(args.mafdir, rg.chrom + ".mafindex"),
os.path.join(args.mafdir, rg.chrom + ".maf"),
args.organism + "." + rg.chrom)
exon_s = []
exon_e = []
if rg.data:
data = rg.data.split("\t")
if len(data) == 7 and int(data[4]) > 1:
z = rg.extract_blocks()
for g in z:
exon_s.append(g.initial)
def test_old(self):
idx = MafIndex("MAF/ucsc_mm9_chr10.mafindex",
"MAF/ucsc_mm9_chr10.maf", "mm9.chr10")
self.assertEqual(len(idx), 48)
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)
