本文整理汇总了Python中Bio.AlignIO.MafIO.MafIndex类的典型用法代码示例。如果您正苦于以下问题：Python MafIndex类的具体用法？Python MafIndex怎么用？Python MafIndex使用的例子？那么恭喜您, 这里精选的类代码示例或许可以为您提供帮助。
在下文中一共展示了MafIndex类的10个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: main
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 示例2: TestSearchBadMAF
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)示例3: TestSpliceGoodMAF
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)示例4: test_ucscbin
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))示例5: test_region2bin
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))示例6: enumerate
#"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)示例7: setUp
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)示例8: TestSearchGoodMAF
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]))示例9: TestGetRecord
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):
#.........这里部分代码省略.........
示例10: TestSearchGoodMAF
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
#.........这里部分代码省略.........