nioushasadjadi
commited on
Commit
·
1bbc46c
1
Parent(s):
477c08b
First version of BarcodeBERT kmer tokenizer
Browse files- tokenizer.json +286 -0
- tokenizer_config.json +27 -0
tokenizer.json
ADDED
@@ -0,0 +1,286 @@
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1 |
+
{
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"version": "1.0",
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"added_tokens": [
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{
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"id": 0,
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"content": "[MASK]",
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"special": true
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},
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{
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"id": 1,
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"content": "[UNK]",
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"special": true
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}
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],
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"pre_tokenizer": {
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"type": "KmerSplitter",
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"k": 4,
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"stride": 4
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},
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"model": {
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"type": "k-mer",
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"k": 4,
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"stride": 4,
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"unk_token": "[UNK]",
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"vocab": {
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"[MASK]": 0,
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"[UNK]": 1,
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"AAAA": 2,
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+
"AAAC": 3,
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"AAAG": 4,
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"AAAT": 5,
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"AACA": 6,
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"AACC": 7,
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"AACG": 8,
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"AACT": 9,
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"AAGA": 10,
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"AAGC": 11,
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"AAGG": 12,
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"AAGT": 13,
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"AATA": 14,
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"AATC": 15,
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"AATG": 16,
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"AATT": 17,
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"ACAA": 18,
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"ACAC": 19,
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"ACAG": 20,
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"ACAT": 21,
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"ACCA": 22,
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"ACCC": 23,
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"ACCG": 24,
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"ACCT": 25,
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"ACGA": 26,
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"ACGC": 27,
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"ACGG": 28,
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"ACGT": 29,
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"ACTA": 30,
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"ACTC": 31,
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"ACTG": 32,
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"ACTT": 33,
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"AGAA": 34,
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"AGAC": 35,
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"AGAG": 36,
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"AGAT": 37,
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"AGCA": 38,
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"AGCC": 39,
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"AGCG": 40,
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"AGCT": 41,
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"AGGA": 42,
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"AGGC": 43,
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"AGGG": 44,
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"AGGT": 45,
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"AGTA": 46,
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"AGTC": 47,
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"AGTG": 48,
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"AGTT": 49,
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"ATAA": 50,
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"ATAC": 51,
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"ATAG": 52,
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"ATAT": 53,
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"ATCA": 54,
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"ATCC": 55,
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"ATCG": 56,
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"ATCT": 57,
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"ATGA": 58,
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"ATGC": 59,
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"ATGG": 60,
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"ATGT": 61,
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"ATTA": 62,
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"ATTC": 63,
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"ATTG": 64,
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"ATTT": 65,
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"CAAA": 66,
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"CAAC": 67,
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"CAAG": 68,
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"CAAT": 69,
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"CACA": 70,
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"CACC": 71,
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"CACG": 72,
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"CACT": 73,
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"CAGA": 74,
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"CAGC": 75,
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"CAGG": 76,
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"CAGT": 77,
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"CATA": 78,
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"CATC": 79,
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"CATG": 80,
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"CATT": 81,
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"CCAA": 82,
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"CCAC": 83,
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"CCAG": 84,
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"CCAT": 85,
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"CCCA": 86,
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"CCCC": 87,
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"CCCG": 88,
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"CCCT": 89,
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"CCGA": 90,
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"CCGC": 91,
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"CCGG": 92,
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"CCGT": 93,
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"CCTA": 94,
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"CCTC": 95,
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"CCTG": 96,
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"CCTT": 97,
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"CGAA": 98,
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"CGAC": 99,
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"CGAG": 100,
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"CGAT": 101,
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"CGCA": 102,
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"CGCC": 103,
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"CGCG": 104,
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"CGCT": 105,
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"CGGA": 106,
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"CGGC": 107,
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"CGGG": 108,
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"CGGT": 109,
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"CGTA": 110,
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"CGTC": 111,
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"CGTG": 112,
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"CGTT": 113,
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"CTAA": 114,
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"CTAC": 115,
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"CTAG": 116,
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"CTAT": 117,
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"CTCA": 118,
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"CTCC": 119,
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+
"CTCG": 120,
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147 |
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"CTCT": 121,
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"CTGA": 122,
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149 |
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"CTGC": 123,
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"CTGG": 124,
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"CTGT": 125,
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"CTTA": 126,
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"CTTC": 127,
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"CTTG": 128,
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"CTTT": 129,
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"GAAA": 130,
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"GAAC": 131,
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"GAAG": 132,
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"GAAT": 133,
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"GACA": 134,
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"GACC": 135,
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"GACG": 136,
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"GACT": 137,
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"GAGA": 138,
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"GAGC": 139,
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"GAGG": 140,
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"GAGT": 141,
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"GATA": 142,
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"GATC": 143,
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"GATG": 144,
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"GATT": 145,
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"GCAA": 146,
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"GCAC": 147,
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"GCAG": 148,
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"GCAT": 149,
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"GCCA": 150,
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"GCCC": 151,
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"GCCG": 152,
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"GCCT": 153,
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"GCGA": 154,
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"GCGC": 155,
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"GCGG": 156,
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"GCGT": 157,
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"GCTA": 158,
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"GCTC": 159,
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"GCTG": 160,
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+
"GCTT": 161,
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+
"GGAA": 162,
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+
"GGAC": 163,
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+
"GGAG": 164,
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+
"GGAT": 165,
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192 |
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"GGCA": 166,
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+
"GGCC": 167,
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194 |
+
"GGCG": 168,
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195 |
+
"GGCT": 169,
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"GGGA": 170,
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197 |
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"GGGC": 171,
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198 |
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"GGGG": 172,
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199 |
+
"GGGT": 173,
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"GGTA": 174,
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"GGTC": 175,
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202 |
+
"GGTG": 176,
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203 |
+
"GGTT": 177,
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"GTAA": 178,
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"GTAC": 179,
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+
"GTAG": 180,
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"GTAT": 181,
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208 |
+
"GTCA": 182,
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"GTCC": 183,
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"GTCG": 184,
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"GTCT": 185,
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"GTGA": 186,
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213 |
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"GTGC": 187,
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214 |
+
"GTGG": 188,
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215 |
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"GTGT": 189,
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216 |
+
"GTTA": 190,
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217 |
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"GTTC": 191,
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218 |
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"GTTG": 192,
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219 |
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"GTTT": 193,
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220 |
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"TAAA": 194,
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"TAAC": 195,
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+
"TAAG": 196,
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"TAAT": 197,
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224 |
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"TACA": 198,
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225 |
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"TACC": 199,
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226 |
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"TACG": 200,
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227 |
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"TACT": 201,
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"TAGA": 202,
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"TAGC": 203,
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"TAGG": 204,
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"TAGT": 205,
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"TATA": 206,
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233 |
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"TATC": 207,
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"TATG": 208,
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"TATT": 209,
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"TCAA": 210,
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"TCAC": 211,
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238 |
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"TCAG": 212,
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"TCAT": 213,
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"TCCA": 214,
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"TCCC": 215,
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"TCCG": 216,
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"TCCT": 217,
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"TCGA": 218,
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245 |
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"TCGC": 219,
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"TCGG": 220,
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247 |
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"TCGT": 221,
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"TCTA": 222,
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249 |
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"TCTC": 223,
|
250 |
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"TCTG": 224,
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251 |
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"TCTT": 225,
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252 |
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"TGAA": 226,
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253 |
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"TGAC": 227,
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254 |
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"TGAG": 228,
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255 |
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"TGAT": 229,
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256 |
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"TGCA": 230,
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257 |
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"TGCC": 231,
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258 |
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"TGCG": 232,
|
259 |
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"TGCT": 233,
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260 |
+
"TGGA": 234,
|
261 |
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"TGGC": 235,
|
262 |
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"TGGG": 236,
|
263 |
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"TGGT": 237,
|
264 |
+
"TGTA": 238,
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265 |
+
"TGTC": 239,
|
266 |
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"TGTG": 240,
|
267 |
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"TGTT": 241,
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268 |
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"TTAA": 242,
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269 |
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"TTAC": 243,
|
270 |
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"TTAG": 244,
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271 |
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"TTAT": 245,
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272 |
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"TTCA": 246,
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273 |
+
"TTCC": 247,
|
274 |
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"TTCG": 248,
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275 |
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"TTCT": 249,
|
276 |
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"TTGA": 250,
|
277 |
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"TTGC": 251,
|
278 |
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"TTGG": 252,
|
279 |
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"TTGT": 253,
|
280 |
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"TTTA": 254,
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281 |
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"TTTC": 255,
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282 |
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"TTTG": 256,
|
283 |
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"TTTT": 257
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}
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}
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}
|
tokenizer_config.json
ADDED
@@ -0,0 +1,27 @@
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{
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"added_tokens_decoder": {
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"0": {
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"content": "[MASK]",
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"lstrip": false,
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"normalized": false,
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7 |
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"rstrip": false,
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"single_word": false,
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"special": true
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},
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"1": {
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"content": "[UNK]",
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"lstrip": false,
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"normalized": false,
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"rstrip": false,
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"single_word": false,
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"special": true
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}
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},
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"clean_up_tokenization_spaces": true,
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"mask_token": "[MASK]",
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"model_max_length": 1000000000000.0,
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"tokenizer_class": "KmerTokenizer",
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"unk_token": "[UNK]",
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"k": 4,
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"stride": 4
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}
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