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from Bio.SeqUtils.CodonUsage import CodonAdaptationIndex
cai = CodonAdaptationIndex()
# https://github.com/yanlinlin82/EMBOSS/blob/master/emboss/data/CODONS/Eyeastcai.cut
Eyeastcai_cut = """\
TAG * 0.040 0.170 1
TGA * 0.040 0.170 1
TAA * 0.920 3.820 22
GCG A 0.000 0.000 0
GCA A 0.010 1.040 6
GCC A 0.240 22.420 130
GCT A 0.750 71.610 411
TGC C 0.070 0.520 3
TGT C 0.930 6.610 39
GAT D 0.360 19.640 112
GAC D 0.640 34.940 202
GAG E 0.020 1.220 5
GAA E 0.980 52.670 305
TTT F 0.100 3.300 19
TTC F 0.900 29.200 168
GGA G 0.000 0.170 1
GGG G 0.000 0.350 2
GGC G 0.020 1.560 9
GGT G 0.970 79.610 459
CAT H 0.200 4.350 25
CAC H 0.800 17.730 102
ATA I 0.000 0.000 0
ATT I 0.460 26.070 149
ATC I 0.540 31.110 181
AAA K 0.120 11.120 65
AAG K 0.880 84.130 483
CTC L 0.000 0.000 1
CTG L 0.000 0.170 1
CTT L 0.000 0.350 2
CTA L 0.030 2.430 14
TTA L 0.100 7.470 42
TTG L 0.860 62.400 359
ATG M 1.000 18.950 109
AAT N 0.050 1.910 11
AAC N 0.950 36.160 208
CCG P 0.000 0.000 0
CCC P 0.010 0.350 2
CCT P 0.040 1.740 10
CCA P 0.950 36.680 211
CAG Q 0.000 0.000 1
CAA Q 1.000 26.590 153
CGA R 0.000 0.000 0
CGC R 0.000 0.000 0
CGG R 0.000 0.000 0
AGG R 0.000 0.170 1
CGT R 0.120 7.650 43
AGA R 0.870 54.580 314
TCG S 0.000 0.170 1
AGT S 0.010 0.700 4
AGC S 0.020 1.040 6
TCA S 0.020 1.220 7
TCC S 0.380 22.940 133
TCT S 0.560 33.720 192
ACG T 0.000 0.170 1
ACA T 0.010 0.350 2
ACT T 0.470 25.900 151
ACC T 0.520 28.680 164
GTA V 0.000 0.000 0
GTG V 0.010 0.700 5
GTC V 0.450 40.150 231
GTT V 0.540 48.500 278
TGG W 1.000 8.170 47
TAT Y 0.060 1.560 10
TAC Y 0.940 24.680 141"""
w = {}
for line in Eyeastcai_cut.splitlines():
trip, aa, we, fr, x = line.split()
w[trip] = float(we)
cai.set_cai_index(w)
S = "CGACGCCGGCGACGCCGGCGACGCCGGCGACGCCGG"
S = "ATGATGATGATGATGATGATGATGATGATG"
cai.cai_for_gene(S)
import CAI
CAI.CAI(S, weights=w)
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