cobot-tools 0.1.2.0 → 0.1.2.1

raw patch · 3 files changed

+8/−5 lines, 3 files

Files

• ChangeLog.md +4/−0
• cobot-tools.cabal +2/−2
• src/Bio/Tools/Sequence/CodonOptimization/Types.hs +2/−3

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.2.1] - 2019-12-9+### Changed+- changed `forbidden` parameter type+ ## [0.1.2.0] - 2019-12-5 ### Added - wrike-426952824 : added Ecoli and CHO codon tables

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: ea5b0488b2bf324cf7921fa277e07d923d6a1eee5bb0f9e6a940db2753897610+-- hash: f2ccf441623f2e23d11376c3e75ce4d4f1cdd056329f2470c7113e541c1dddcb  name:           cobot-tools-version:        0.1.2.0+version:        0.1.2.1 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

@@ -5,7 +5,6 @@     , defaultForbiddenRegexp     ) where -import qualified Data.ByteString.Lazy as BSL (ByteString) import           Data.Default                (Default (..)) import           GHC.Generics                (Generic) @@ -30,14 +29,14 @@         , rnaFoldingWindow   :: Int                -- ^ length of the window for RNA folding score calculation (bp)         , forbiddenDNAWeight :: Double             -- ^ forbidden DNA motifs score weight         , gcContentDesired   :: Int                -- ^ desired gc content in percents-        , forbiddenSequence  :: [BSL.ByteString]   -- ^ list of forbidden patterns+        , forbiddenSequence  :: [String]           -- ^ list of forbidden patterns         }     deriving (Eq, Show, Generic)  instance Default CodonScoreConfig where   def = CodonScoreConfig CHO 3 1 1 0.5 1.4 40 0.001 2.6 100 1 43 defaultForbiddenRegexp -defaultForbiddenRegexp :: [BSL.ByteString]+defaultForbiddenRegexp :: [String] defaultForbiddenRegexp =     [ "ATTTA"     , "ATACTCCCCC"