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'
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'
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
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
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"
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"