cobot-tools 0.1.2.1 → 0.1.2.2
raw patch · 4 files changed
+25/−21 lines, 4 files
Files
- ChangeLog.md +4/−0
- cobot-tools.cabal +2/−2
- src/Bio/Tools/Sequence/CodonOptimization/Constants.hs +18/−18
- test/SpecCodonOptimization.hs +1/−1
ChangeLog.md view
@@ -2,6 +2,10 @@ ## [Unreleased] +## [0.1.2.2] - 2019-12-25+### Fixed+- wrike-438378826: CHO codon table fixed+ ## [0.1.2.1] - 2019-12-9 ### Changed - changed `forbidden` parameter type
cobot-tools.cabal view
@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: f2ccf441623f2e23d11376c3e75ce4d4f1cdd056329f2470c7113e541c1dddcb+-- hash: 84a7b89a1041e9805b22b527f40e7624a4313d166c84a98dae62d1025b096246 name: cobot-tools-version: 0.1.2.1+version: 0.1.2.2 synopsis: Biological data file formats and IO description: Please see the README on GitHub at <https://github.com/less-wrong/cobot-tools#readme> category: Bio
src/Bio/Tools/Sequence/CodonOptimization/Constants.hs view
@@ -167,26 +167,26 @@ -- taken from https://www.genscript.com/tools/codon-frequency-table ak2MaxFrequCodon CHO = fromList- [ (ALA, ([DG, DC, DC], 0.26))- , (CYS, ([DT, DG, DC], 0.54))- , (ASP, ([DG, DA, DT], 0.63))- , (GLU, ([DG, DA, DA], 0.68))- , (PHE, ([DT, DT, DT], 0.58))- , (GLY, ([DG, DG, DC], 0.37))- , (HIS, ([DC, DA, DT], 0.57))- , (ILE, ([DA, DT, DT], 0.49))- , (LYS, ([DA, DA, DA], 0.74))- , (LEU, ([DC, DT, DG], 0.47))+ [ (ALA, ([DG, DC, DC], 0.37))+ , (CYS, ([DT, DG, DC], 0.53))+ , (ASP, ([DG, DA, DC], 0.53))+ , (GLU, ([DG, DA, DG], 0.59))+ , (PHE, ([DT, DT, DC], 0.53))+ , (GLY, ([DG, DG, DC], 0.34))+ , (HIS, ([DC, DA, DC], 0.56))+ , (ILE, ([DA, DT, DC], 0.51))+ , (LYS, ([DA, DA, DG], 0.61))+ , (LEU, ([DC, DT, DG], 0.39)) , (MET, ([DA, DT, DG], 1.0))- , (ASN, ([DA, DA, DC], 0.51))- , (PRO, ([DC, DC, DG], 0.49))- , (GLN, ([DC, DA, DG], 0.66))- , (ARG, ([DC, DG, DC], 0.36))- , (SER, ([DA, DG, DC], 0.25))- , (THR, ([DA, DC, DC], 0.4))- , (VAL, ([DG, DT, DG], 0.35))+ , (ASN, ([DA, DA, DC], 0.55))+ , (PRO, ([DC, DC, DC], 0.32))+ , (GLN, ([DC, DA, DG], 0.76))+ , (ARG, ([DC, DG, DG], 0.19))+ , (SER, ([DA, DG, DC], 0.22))+ , (THR, ([DA, DC, DC], 0.37))+ , (VAL, ([DG, DT, DG], 0.46)) , (TRP, ([DT, DG, DG], 1.0))- , (TYR, ([DT, DA, DT], 0.59))+ , (TYR, ([DT, DA, DC], 0.56)) ] codonFrequencies :: Organism -> Map [DNA] Double
test/SpecCodonOptimization.hs view
@@ -120,7 +120,7 @@ nk <- toRandomNKSequ ak let res = optimizeAA confCHO ak - res `shouldBe` "GCCAGCACCAAGGGCCCCAGCGTGTTTCCTCTGGCCCCTTCTTCTAAGTCTACCTCTGGCGGCACCGCCGCCCTGGGCTGTCTGGTGAAGGATTACTTTCCTGAGCCTGTGACCGTGTCTTGGAACTCTGGCGCCCTGACCTCTGGCGTGCACACCTTTCCTGCCGTGCTGCAGTCTTCTGGCCTGTACTCTCTGTCTTCTGTGGTGACCGTGCCTTCTTCTTCTCTGGGCACCCAGACCTACATCTGCAACGTGAACCACAAGCCTTCTAACACCAAGGTGGACAAGAAGGTG"+ res `shouldBe` "GCCAGCACCAAGGGCCCCAGCGTGTTTCCTCTGGCCCCTTCTTCTAAGTCTACCTCTGGCGGCACCGCCGCCCTGGGCTGTCTGGTGAAGGATTACTTCCCTGAGCCTGTGACCGTGTCTTGGAACTCTGGCGCCCTGACCTCTGGCGTGCACACCTTCCCTGCCGTGCTGCAGTCTTCTGGCCTGTACTCTCTGTCTTCTGTGGTGACCGTGCCTTCTTCTTCTCTGGGCACCCAGACCTACATCTGCAACGTGAACCACAAGCCTTCTAACACCAAGGTGGACAAGAAGGTG" res `assertScoreByCHOBetterThan` nk optimizeSequenceForEColi :: Spec