Python map_to_cigar示例

示例#1

文件： test_cigar.py 项目： miklou/pycogent

 def setUp(self):
     self.cigar_text = '3D2M3D6MDM2D3MD'
     self.aln_seq = DNA.makeSequence('---AA---GCTTAG-A--CCT-')
     self.aln_seq1 = DNA.makeSequence('CCAAAAAA---TAGT-GGC--G')
     self.map, self.seq = self.aln_seq.parseOutGaps()
     self.map1, self.seq1 = self.aln_seq1.parseOutGaps()
     self.slices = [(1, 4), (0, 8), (7, 12), (0, 1), (3, 5)]
     self.aln = LoadSeqs(data = {"FAKE01": self.aln_seq, "FAKE02": self.aln_seq1})
     self.cigars = {"FAKE01": self.cigar_text, "FAKE02": map_to_cigar(self.map1)}
     self.seqs = {"FAKE01": str(self.seq), "FAKE02": str(self.seq1)}

示例#2

 def setUp(self):
     self.cigar_text = '3D2M3D6MDM2D3MD'
     self.aln_seq = DNA.makeSequence('---AA---GCTTAG-A--CCT-')
     self.aln_seq1 = DNA.makeSequence('CCAAAAAA---TAGT-GGC--G')
     self.map, self.seq = self.aln_seq.parseOutGaps()
     self.map1, self.seq1 = self.aln_seq1.parseOutGaps()
     self.slices = [(1, 4), (0, 8), (7, 12), (0, 1), (3, 5)]
     self.aln = LoadSeqs(data = {"FAKE01": self.aln_seq, "FAKE02": self.aln_seq1})
     self.cigars = {"FAKE01": self.cigar_text, "FAKE02": map_to_cigar(self.map1)}
     self.seqs = {"FAKE01": str(self.seq), "FAKE02": str(self.seq1)}

示例#3

文件： test_cigar.py 项目： miklou/pycogent

 def test_map_to_cigar(self):
     """convert a Map to cigar string"""
     assert map_to_cigar(self.map) == self.cigar_text

示例#4

 def test_map_to_cigar(self):
     """convert a Map to cigar string"""
     assert map_to_cigar(self.map) == self.cigar_text