How to use the cutadapt.colorspace.encode function in cutadapt
To help you get started, we’ve selected a few cutadapt examples, based on popular ways it is used in public projects.
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marcelm / cutadapt / tests / test_colorspace.py View on Github 
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("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"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"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'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"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"cutadapt
Adapter trimming and other preprocessing of high-throughput sequencing reads
Package Health Score
81 / 100Popular cutadapt functions
- cutadapt.__main__.main
- cutadapt.__main__.parse_lengths
- cutadapt.adapters.BackAdapter
- cutadapt.adapters.PrefixAdapter
- cutadapt.adapters.warn_duplicate_adapters
- cutadapt.align.Aligner
- cutadapt.colorspace.encode
- cutadapt.modifiers.AdapterCutter
- cutadapt.modifiers.ModificationInfo
- cutadapt.modifiers.QualityTrimmer
- cutadapt.modifiers.Shortener
- cutadapt.modifiers.UnconditionalCutter
- cutadapt.parser.AdapterParser
- cutadapt.parser.AdapterSpecification
- cutadapt.seqio.FastaReader
- cutadapt.seqio.FastaWriter
- cutadapt.seqio.FastqReader
- cutadapt.seqio.find_fastq_record_end
- cutadapt.seqio.open
- cutadapt.seqio.Sequence