cobot-tools 0.1.2.2 → 0.1.2.3

raw patch · 3 files changed

+35/−5 lines, 3 files

Files

• ChangeLog.md +4/−0
• cobot-tools.cabal +2/−2
• test/SpecCodonOptimization.hs +29/−3

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.2.3] - 2019-12-29+### Added+- quick-check tests for codon-optimization algorithm+ ## [0.1.2.2] - 2019-12-25 ### Fixed - wrike-438378826: CHO codon table fixed

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 84a7b89a1041e9805b22b527f40e7624a4313d166c84a98dae62d1025b096246+-- hash: c103fb434308ace7b65d824296158feae6828093d573662118d87fb7438dba25  name:           cobot-tools-version:        0.1.2.2+version:        0.1.2.3 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

@@ -2,7 +2,7 @@  module SpecCodonOptimization where -import           Bio.NucleicAcid.Nucleotide.Type                (DNA)+import           Bio.NucleicAcid.Nucleotide.Type                (DNA (..)) import           Bio.Protein.AminoAcid                          () import           Bio.Protein.AminoAcid.Type                     (AA) import           Bio.Tools.Sequence.CodonOptimization.Algo      (optimizeAA,@@ -11,9 +11,10 @@                                                                  scoreCmp,                                                                  scoreSequence) import           Bio.Tools.Sequence.CodonOptimization.Constants (ak2Codon)-import           Bio.Tools.Sequence.CodonOptimization.Types     (CodonScoreConfig(..),+import           Bio.Tools.Sequence.CodonOptimization.Types     (CodonScoreConfig (..),                                                                  Organism (..),                                                                  defaultForbiddenRegexp)+import           Control.Monad                                  (replicateM) import           Data.List                                      (foldl',                                                                  maximumBy,                                                                  minimumBy)@@ -22,8 +23,13 @@ import           System.Random import           Test.Hspec                                     (Expectation,                                                                  Spec, describe,-                                                                 it, shouldBe,+                                                                 it, runIO,+                                                                 shouldBe,                                                                  shouldSatisfy)+import           Test.Hspec.QuickCheck                          (prop)+import           Test.QuickCheck.Gen                            (Gen, elements)+import           Test.QuickCheck.Property                       (Property,+                                                                 forAll)  confHuman :: CodonScoreConfig confHuman = CodonScoreConfig Human 3 1 1 0.5 1.4 40 0.001 2.6 100 1 60 defaultForbiddenRegexp@@ -67,6 +73,9 @@ codonOptimizationSpec :: Spec codonOptimizationSpec =     describe "Codon optimization spec" $ do+        optimizedAgainstRandom confCHO+        optimizedAgainstRandom confHuman+        optimizedAgainstRandom confEColi         optimizeSequence         optimizeSequenceForEColi         optimizeSequenceForCHO@@ -312,3 +321,20 @@         score conf' "GCCAGCGGCGACAAGACCCACACCTGTCCT" `shouldBe` 80.74362252733329         score conf' "CCCTGCCCCGCCCCCGAGGCCGCCGGCGGCCCTAGCGTGTTCCTGTTCCCTCCTAAGCCTAAGGACACCCTGATGATCAGCAGAACCCCCGAGGTGACCTGCGTGGTGGTGGACGTGAGCCACGAGGACCCTGAGGTGAAGTTCAATTGGTACGTGGACGGCGTGGAGGTGCACAACGCCAAGACCAAGCCTAGAGAGGAGCAGTACAACAGCACCTACAGAGTGGTGAGCGTGCTGACCGTGCTGCACCAAGACTGGCTGAACGGCAAGGAGTACAAGTGCAAGGTGAGCAACAAGGCCCTGCCCGCCCCTATCGAGAAGACCATCAGCAAGGCCAAG"          `shouldBe` 96.19662511761598++optimizedAgainstRandom :: CodonScoreConfig -> Spec+optimizedAgainstRandom conf = describe "optimizedAgainstRandom" $ do+        let ak = "GQPREPQVYTLPPSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK"+        gen <- runIO $ genNKSequence ak+        prop "optimized sequence should have better score than any random sequence" (runBatchCheck ak gen)+  where+    runBatchCheck :: [AA] -> Gen [DNA] -> Property+    runBatchCheck ak gen = forAll gen (\nk -> scoreSequence conf res >= scoreSequence conf nk)+      where+        res = optimizeAA conf ak++genNKSequence :: [AA] -> IO (Gen [DNA])+genNKSequence aa = elements <$> variants aa++variants :: [AA] -> IO [[DNA]]+variants aa = replicateM 100 (toRandomNKSequ aa)