本文整理匯總了Python中Bio.AlignIO.MafIO.MafIndex.get_spliced方法的典型用法代碼示例。如果您正苦於以下問題：Python MafIndex.get_spliced方法的具體用法？Python MafIndex.get_spliced怎麽用？Python MafIndex.get_spliced使用的例子？那麽, 這裏精選的方法代碼示例或許可以為您提供幫助。您也可以進一步了解該方法所在類Bio.AlignIO.MafIO.MafIndex的用法示例。
在下文中一共展示了MafIndex.get_spliced方法的4個代碼示例，這些例子默認根據受歡迎程度排序。您可以為喜歡或者感覺有用的代碼點讚，您的評價將有助於係統推薦出更棒的Python代碼示例。
示例1: TestSpliceGoodMAF
# 需要導入模塊: from Bio.AlignIO.MafIO import MafIndex [as 別名]
# 或者: from Bio.AlignIO.MafIO.MafIndex import get_spliced [as 別名]
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2: main
# 需要導入模塊: from Bio.AlignIO.MafIO import MafIndex [as 別名]
# 或者: from Bio.AlignIO.MafIO.MafIndex import get_spliced [as 別名]
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3: enumerate
# 需要導入模塊: from Bio.AlignIO.MafIO import MafIndex [as 別名]
# 或者: from Bio.AlignIO.MafIO.MafIndex import get_spliced [as 別名]
exon_s.append(g.initial)
exon_e.append(g.final)
else:
exon_s = [rg.initial]
exon_e = [rg.final]
else:
exon_s = [rg.initial]
exon_e = [rg.final]
if rg.orientation == "+":
strand = "+1"
else:
strand = "-1"
multiple_alignment = idx.get_spliced(exon_s,
exon_e,
strand = strand)
for j, seqrec in enumerate(multiple_alignment):
if seqrec.id.startswith(args.organism):
if j == 0: break
else:
multiple_alignment._records[0], multiple_alignment._records[j] = multiple_alignment._records[j], multiple_alignment._records[0]
#print(dir(multiple_alignment))
#sys.exit(0)
seqs = []
for seqrec in multiple_alignment:
#print(dir(seqrec))
try:示例4: TestSearchGoodMAF
# 需要導入模塊: from Bio.AlignIO.MafIO import MafIndex [as 別名]
# 或者: from Bio.AlignIO.MafIO.MafIndex import get_spliced [as 別名]
#.........這裏部分代碼省略.........
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