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from CAI import CAI
import pytest
import math
"""
The CAI is calculated for the E. coli rpsU gene given as an example on
page 1285 in Sharp 1987. This sequence is available from
Genbank (NC_000913 REGION: 3210781..3210996).
atg ccg gta att aaa gta cgtgaaaacgagccgttcgacgtagctctgcgtcgctt
||| ||| ||| ||| |||
.CCG.GTA.ATT.AAA.GTA.
caagcgttcctgcgaaaaagcaggtgttctggcggaagttcgtcgtcgtgagttctatgaaa
aaccgactaccgaacgtaagcgcgctaaagcttctgcagtgaaacgtcacgcgaagaaactg
gctcgcgaaaacgcacgccgcactcgtctgtactaa
"""
def test_sharp1987_fig():
sharp_table_1 = """\
AA Tri RSCUe we RSCUy wy
Phe TTT 0.456 0.296 0.203 0.113
Phe TTC 1.544 1.000 1.797 1.000
Leu TTA 0.106 0.020 0.601 0.117
Leu TTG 0.106 0.020 5.141 1.000
Leu CTT 0.225 0.042 0.029 0.006
Leu CTC 0.198 0.037 0.014 0.003
Leu CTA 0.040 0.007 0.200 0.039
Leu CTG 5.326 1.000 0.014 0.003
Ile ATT 0.466 0.185 1.352 0.823
Ile ATC 2.525 1.000 1.643 1.000
Ile ATA 0.008 0.003 0.005 0.003
Met ATG 1.000 1.000 1.000 1.000
Val GTT 2.244 1.000 2.161 1.000
Val GTC 0.148 0.066 1.796 0.831
Val GTA 1.111 0.495 0.004 0.002
Val GTG 0.496 0.221 0.039 0.018
Ser TCT 2.571 1.000 3.359 1.000
Ser TCC 1.912 0.744 2.327 0.693
Ser TCA 0.198 0.077 0.122 0.036
Ser TCG 0.044 0.017 0.017 0.005
Pro CCT 0.231 0.070 0.179 0.047
Pro CCC 0.038 0.012 0.036 0.009
Pro CCA 0.442 0.135 3.776 1.000
Pro CCG 3.288 1.000 0.009 0.002
Thr ACT 1.804 0.965 1.899 0.921
Thr ACC 1.870 1.000 2.063 1.000
Thr ACA 0.141 0.076 0.025 0.012
Thr ACG 0.185 0.099 0.013 0.006
Ala GCT 1.877 1.000 3.005 1.000
Ala GCC 0.228 0.122 0.948 0.316
Ala GCA 1.099 0.586 0.044 0.015
Ala GCG 0.796 0.424 0.004 0.001
Tyr TAT 0.386 0.239 0.132 0.071
Tyr TAC 1.614 1.000 1.868 1.000
His CAT 0.451 0.291 0.394 0.245
His CAC 1.549 1.000 1.606 1.000
Gln CAA 0.220 0.124 1.987 1.000
Gln CAG 1.780 1.000 0.013 0.007
Asn AAT 0.097 0.051 0.100 0.053
Asn AAC 1.903 1.000 1.900 1.000
Lys AAA 1.596 1.000 0.237 0.135
Lys AAG 0.404 0.253 1.763 1.000
Asp GAT 0.605 0.434 0.713 0.554
Asp GAC 1.395 1.000 1.287 1.000
Glu GAA 1.589 1.000 1.968 1.000
Glu GAG 0.411 0.259 0.032 0.016
Cys TGT 0.667 0.500 1.857 1.000
Cys TGC 1.333 1.000 0.143 0.077
Trp TGG 1.000 1.000 1.000 1.000
Arg CGT 4.380 1.000 0.718 0.137
Arg CGC 1.561 0.356 0.008 0.002
Arg CGA 0.017 0.004 0.008 0.002
Arg CGG 0.017 0.004 0.008 0.002
Ser AGT 0.220 0.085 0.070 0.021
Ser AGC 1.055 0.410 0.105 0.031
Arg AGA 0.017 0.004 5.241 1.000
Arg AGG 0.008 0.002 0.017 0.003
Gly GGT 2.283 1.000 3.898 1.000
Gly GGC 1.652 0.724 0.077 0.020
Gly GGA 0.022 0.010 0.009 0.002
Gly GGG 0.043 0.019 0.017 0.004"""
we = {}
for line in sharp_table_1.splitlines()[1:]:
_, cdn,_ , w, *_ = line.split()
we[cdn] = float(w)
rpsU = ("atgccggtaattaaagtacgtgaaaacgagccgttcgacgtagctctgcgtcgctt"
"caagcgttcctgcgaaaaagcaggtgttctggcggaagttcgtcgtcgtgagttct"
"atgaaaaaccgactaccgaacgtaagcgcgctaaagcttctgcagtgaaacgtcac"
"gcgaagaaactggctcgcgaaaacgcacgccgcactcgtctgtactaa")
assert math.isclose(CAI(rpsU, weights=we),
0.7260113974828158)
|
