当前位置: 首页>>代码示例>>Python>>正文


Python MafIO.MafIndex类代码示例

本文整理汇总了Python中Bio.AlignIO.MafIO.MafIndex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, 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 
开发者ID:jqujqu,项目名称:jqujqu_python_scripts,代码行数:51,代码来源:maf2pid.py

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)
开发者ID:BioGeek,项目名称:biopython,代码行数:11,代码来源:test_MafIO_index.py

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)
开发者ID:BioGeek,项目名称:biopython,代码行数:41,代码来源:test_MafIO_index.py

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))
开发者ID:BioGeek,项目名称:biopython,代码行数:17,代码来源:test_MafIO_index.py

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))
开发者ID:BioGeek,项目名称:biopython,代码行数:17,代码来源:test_MafIO_index.py

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)
开发者ID:Marvin84,项目名称:reg-gen,代码行数:31,代码来源:phylocsf_check.py

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)
开发者ID:BioGeek,项目名称:biopython,代码行数:4,代码来源:test_MafIO_index.py

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]))
开发者ID:BioGeek,项目名称:biopython,代码行数:87,代码来源:test_MafIO_index.py

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.........
开发者ID:BioGeek,项目名称:biopython,代码行数:101,代码来源:test_MafIO_index.py

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.........
开发者ID:andrewguy,项目名称:biopython,代码行数:101,代码来源:test_MafIO_index.py


注:本文中的Bio.AlignIO.MafIO.MafIndex类示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。