Python encode示例

示例#1

文件： test_colorspace.py 项目： raonyguimaraes/atropos

def test_decode():
    for s in sequences:
        expected = s.replace('.', 'N')
        encoded = encode(s)
        assert decode(encoded) == expected
    assert decode('A.') == 'AN'
    assert decode('C.') == 'CN'
    assert decode('G.') == 'GN'
    assert decode('T.') == 'TN'

示例#2

文件： test_colorspace.py 项目： jdidion/atropos

def test_decode():
    for s in sequences:
        expected = s.replace('.', 'N')
        encoded = encode(s)
        assert decode(encoded) == expected
    assert decode('A.') == 'AN'
    assert decode('C.') == 'CN'
    assert decode('G.') == 'GN'
    assert decode('T.') == 'TN'

示例#3

文件： __init__.py 项目： jdidion/atropos

 def __init__(self, *args, **kwargs):
     if kwargs.get('adapter_wildcards', False):
         raise ValueError("Wildcards not supported for colorspace adapters")
     kwargs['adapter_wildcards'] = False
     super().__init__(*args, **kwargs)
     has_nucleotide_seq = False
     if set(self.sequence) <= set('ACGT'):
         # adapter was given in basespace
         self.nucleotide_sequence = self.sequence
         has_nucleotide_seq = True
         self.sequence = cs.encode(self.sequence)[1:]
     if self.where in (PREFIX, FRONT) and not has_nucleotide_seq:
         raise ValueError(
             "A 5' colorspace adapter needs to be given in nucleotide space")
     self.aligner.reference = self.sequence

示例#4

文件： __init__.py 项目： asellappen/atropos

 def __init__(self, *args, **kwargs):
     if kwargs.get('adapter_wildcards', False):
         raise ValueError("Wildcards not supported for colorspace adapters")
     kwargs['adapter_wildcards'] = False
     super().__init__(*args, **kwargs)
     has_nucleotide_seq = False
     if set(self.sequence) <= set('ACGT'):
         # adapter was given in basespace
         self.nucleotide_sequence = self.sequence
         has_nucleotide_seq = True
         self.sequence = cs.encode(self.sequence)[1:]
     if self.where in (PREFIX, FRONT) and not has_nucleotide_seq:
         raise ValueError(
             "A 5' colorspace adapter needs to be given in nucleotide space"
         )
     self.aligner.reference = self.sequence

示例#5

文件： test_colorspace.py 项目： raonyguimaraes/atropos

def test_encode():
    assert encode("AA") == "A0"
    assert encode("AC") == "A1"
    assert encode("AG") == "A2"
    assert encode("AT") == "A3"
    assert encode("CA") == "C1"
    assert encode("CC") == "C0"
    assert encode("CG") == "C3"
    assert encode("CT") == "C2"
    assert encode("GA") == "G2"
    assert encode("GC") == "G3"
    assert encode("GG") == "G0"
    assert encode("GT") == "G1"
    assert encode("TA") == "T3"
    assert encode("TC") == "T2"
    assert encode("TG") == "T1"
    assert encode("TT") == "T0"

    assert encode("TN") == "T4"
    assert encode("NT") == "N4"
    assert encode("NN") == "N4"

    assert encode("ACGGTC") == "A13012"
    assert encode("TTT.N") == "T0044"
    assert encode("TTNT.N") == "T04444"

示例#6

文件： test_colorspace.py 项目： jdidion/atropos

def test_encode():
    assert encode("AA") == "A0"
    assert encode("AC") == "A1"
    assert encode("AG") == "A2"
    assert encode("AT") == "A3"
    assert encode("CA") == "C1"
    assert encode("CC") == "C0"
    assert encode("CG") == "C3"
    assert encode("CT") == "C2"
    assert encode("GA") == "G2"
    assert encode("GC") == "G3"
    assert encode("GG") == "G0"
    assert encode("GT") == "G1"
    assert encode("TA") == "T3"
    assert encode("TC") == "T2"
    assert encode("TG") == "T1"
    assert encode("TT") == "T0"

    assert encode("TN") == "T4"
    assert encode("NT") == "N4"
    assert encode("NN") == "N4"

    assert encode("ACGGTC") == "A13012"
    assert encode("TTT.N") == "T0044"
    assert encode("TTNT.N") == "T04444"