Exemple #1
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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'
Exemple #2
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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'
Exemple #3
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 def __init__(self, *args, **kwargs):
     super(ColorspaceAdapter, self).__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 = colorspace.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
Exemple #4
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 def __init__(self, *args, **kwargs):
     super(ColorspaceAdapter, self).__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 = colorspace.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
Exemple #5
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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"
Exemple #6
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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"