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"