diff --git a/Biobase/GeneticCodes.hs b/Biobase/GeneticCodes.hs new file mode 100644 --- /dev/null +++ b/Biobase/GeneticCodes.hs @@ -0,0 +1,70 @@ + +module Biobase.GeneticCodes + ( module Biobase.GeneticCodes + , module Biobase.GeneticCodes.Types + , fromByteString + , fromFile + , geneticCodes + , translate + ) where + +import Control.Lens +import Control.Monad.Except +import Data.List (find) +import Data.Text (pack) +import Data.Text (Text,isInfixOf,unpack) +import System.Directory (doesFileExist) +import Text.Printf +import System.Exit (exitSuccess) + +import Biobase.GeneticCodes.Embedded +import Biobase.GeneticCodes.Import +import Biobase.GeneticCodes.Translation +import Biobase.GeneticCodes.Types + + + +codeByTableID + ∷ (MonadError String m) + ⇒ [TranslationTable c a] + → Int + → m (TranslationTable c a) +codeByTableID ts i + = maybe (throwError $ printf "No TranslationTable with ID %d found!" i) return + $ find (\t → t^.tableID == i) ts + +codeByTableNameInfix + ∷ (MonadError String m) + ⇒ [TranslationTable c a] + → Text + → m (TranslationTable c a) +codeByTableNameInfix ts n + = maybe (throwError $ printf "No TranslationTable with Name infix %s found!" $ unpack n) return + $ find (\t → n `isInfixOf` (t^.tableName)) ts + +-- | If the given filepath exists, then we try to load the genetic table from +-- the file. This will fail if there is not exactly one genetic table there. If +-- @fp@ is not a file, we try parsing @fp@ as a numeric ID and look for that +-- table. Finally we try finding an infix with that name. +-- +-- This is all slightly "unsafe" but captures the most common scenario where we +-- either load such a table from file or need selection of the correct one. +-- +-- If the given filepath is @"list"@, then a list of table id's and table names +-- is returned. + +fromFileOrCached + ∷ (MonadIO m, MonadError String m) + ⇒ FilePath + → m (TranslationTable Char Char) +fromFileOrCached fp = do + dfe ← liftIO $ doesFileExist fp + if | fp == "list" → do + mapM_ (liftIO . uncurry (printf "%3d %s\n")) [ (t^.tableID,t^.tableName) | t ← geneticCodes ] + liftIO exitSuccess + | dfe → fromFile fp >>= \case + [x] → return x + xs → throwError $ fp ++ " should contain exactly one translation table!" + | [(k,"")] ← reads fp → codeByTableID geneticCodes k + | otherwise → codeByTableNameInfix geneticCodes $ pack fp + diff --git a/Biobase/GeneticCodes/Embedded.hs b/Biobase/GeneticCodes/Embedded.hs new file mode 100644 --- /dev/null +++ b/Biobase/GeneticCodes/Embedded.hs @@ -0,0 +1,16 @@ + +module Biobase.GeneticCodes.Embedded where + +import Control.Monad.Except +import Data.ByteString (ByteString) +import Data.FileEmbed + +import Biobase.GeneticCodes.Import +import Biobase.GeneticCodes.Types + +geneticCodesFile ∷ ByteString +geneticCodesFile = $(embedFile "sources/translation-tables") + +geneticCodes ∷ [TranslationTable Char Char] +geneticCodes = either error id . runExcept $ fromByteString geneticCodesFile + diff --git a/Biobase/GeneticCodes/Import.hs b/Biobase/GeneticCodes/Import.hs new file mode 100644 --- /dev/null +++ b/Biobase/GeneticCodes/Import.hs @@ -0,0 +1,78 @@ + +-- | +-- +-- The tables imported with these functions are from ENA: +-- + +module Biobase.GeneticCodes.Import where + +import Control.Monad.Except +import Data.ByteString.Char8 as BS hiding (unpack,map) +import Data.ByteString.Char8 (ByteString) +import Data.Text.Encoding (decodeUtf8) +import Data.Text.IO as TIO +import Data.Text (Text,unpack) +import Data.Void +import System.Exit +import Text.Megaparsec +import Text.Megaparsec.Char as MC +import Text.Megaparsec.Char.Lexer as MCL + +import Biobase.Types.Codon + +import Biobase.GeneticCodes.Types + + + +type TTParser = Parsec Void Text + +-- | Import translation tables from a given file. In case of parse error, print +-- the error and exit with a failure. + +fromFile + ∷ (MonadIO m, MonadError String m) + ⇒ FilePath + → m [TranslationTable Char Char] +fromFile fp = (liftIO $ BS.readFile fp) >>= fromByteString + +-- | Parse a ByteString with translation tables. + +fromByteString + ∷ (MonadError String m) + ⇒ ByteString + → m [TranslationTable Char Char] +fromByteString bs = case runParser (some parseTranslationTable) "" (decodeUtf8 bs) of + -- Left err → throwError $ parseErrorPretty err -- megaparsec 6.x + Left err → throwError $ errorBundlePretty err -- megaparsec 7.x + Right rs → return rs + +-- | Parses a single translation table. + +parseTranslationTable ∷ TTParser (TranslationTable Char Char) +parseTranslationTable = do + (i,hdr) ← parseHeader + aas ← parseData "amino acids" + starts' ← parseData "start codons" + base1 ← parseData "Base 1" + base2 ← parseData "Base 2" + base3 ← parseData "Base 3" + let triplets = zipWith3 Codon base1 base2 base3 + let starts = map (=='M') starts' + let translations = zipWith3 TranslationElement triplets starts aas + return $ genTranslationTable i hdr translations + +-- | Parse the header, returning the Identifier and the name of the table. + +parseHeader ∷ TTParser (Int,Text) +parseHeader + = (,) <$> (fromIntegral <$> lexeme MC.space decimal) + <* char ':' <* MC.space + <*> takeWhileP Nothing (/= '\n') + <* MC.space + +parseData ∷ Text → TTParser String +parseData t + = string' t <* MC.space + *> (unpack <$> takeP Nothing 64) + <* MC.space + diff --git a/Biobase/GeneticCodes/Translation.hs b/Biobase/GeneticCodes/Translation.hs new file mode 100644 --- /dev/null +++ b/Biobase/GeneticCodes/Translation.hs @@ -0,0 +1,70 @@ + +-- | Abstract translation functionality. Given a genetic code translation table +-- (as provided within this module), provide translation from the nucleotide to +-- the amino acid alphabet. +-- +-- Limited "backtranslation" capabilities are provided. Since this process is +-- lossy, it should only be used in very specific circumstances. +-- +-- TODO Translation from @BioSequence RNA is missing. + +module Biobase.GeneticCodes.Translation where + +import Control.Lens +import qualified Data.Map.Strict as M +import qualified Data.ByteString.Char8 as BS + +import Biobase.Types.BioSequence +import Biobase.Types.Codon + +import Biobase.GeneticCodes.Types + + + +-- | + +class Translation t where + -- | Defines the target type for a given translation input. + type TargetType t ∷ * + -- | Type of the nucleotide characters. + type CodonType t ∷ * + -- | Type of the amino acid characters. + type AAType t ∷ * + -- | Translate from a given type of sequence @t@ into the target type. + translate ∷ TranslationTable (CodonType t) (AAType t) → t → TargetType t + +-- | Very simple translation of individual base triplets. + +instance Translation (Codon Char) where + type TargetType (Codon Char) = Char + type CodonType (Codon Char) = Char + type AAType (Codon Char) = Char + translate tbl t = maybe 'X' _aminoAcid $ M.lookup t (tbl^.codonToAminoAcid) + {-# Inline translate #-} + +-- | Strings of characters are normally very inconvenient but useful in +-- backtracking cases. Fully assumes that the alphabet is DNA. Ignores +-- non-triplets at the end. + +instance Translation String where + type TargetType String = String + type CodonType String = Char + type AAType String = Char + translate tbl = + let go xs | [x,y,z] ← hd = translate tbl (Codon x y z) : go tl + | otherwise = [] + where (hd,tl) = splitAt 3 xs + in go + +-- | Translation of @BioSequence DNA@. The translation tables assume DNA +-- triplets anyway. Biologically there should be a transcription step in +-- between. Ignores non-triplets at the end. + +instance Translation (BioSequence DNA) where + type TargetType (BioSequence DNA) = BioSequence AA + type CodonType (BioSequence DNA) = Char + type AAType (BioSequence DNA) = Char + translate tbl (BioSequence xs) = + let go k = Just (translate tbl $ Codon (BS.index xs k) (BS.index xs (k+1)) (BS.index xs (k+2)) ,k+3) + in BioSequence . fst $ BS.unfoldrN (BS.length xs `div` 3) go 0 + diff --git a/Biobase/GeneticCodes/Types.hs b/Biobase/GeneticCodes/Types.hs new file mode 100644 --- /dev/null +++ b/Biobase/GeneticCodes/Types.hs @@ -0,0 +1,49 @@ + +-- | + +module Biobase.GeneticCodes.Types where + +import Control.Lens +import Data.ByteString.Char8 (ByteString) +import Data.Map.Strict (Map,fromList,fromListWith) +import Data.Text (Text) + +import Biobase.Types.Codon + + + +data TranslationElement c a = TranslationElement + { _baseCodon ∷ !(Codon c) + , _isStartCodon ∷ !Bool + , _aminoAcid ∷ !a + } + deriving (Show) +makeLenses ''TranslationElement + +data TranslationTable c a = TranslationTable + { _codonToAminoAcid ∷ !(Map (Codon c) (TranslationElement c a)) + , _aminoAcidtoCodons ∷ !(Map a [TranslationElement c a]) + , _tableID ∷ !Int + , _tableName ∷ !Text + } + deriving (Show) +makeLenses ''TranslationTable + +genTranslationTable + ∷ (Ord c, Ord a) + ⇒ Int + -- ^ table identifier + → Text + -- ^ table hdr / table name + → [TranslationElement c a] + -- ^ known translation elements (should be @4^3@ but is not checked) + → TranslationTable c a + -- ^ finished translation table +{-# Inlinable genTranslationTable #-} +genTranslationTable i hdr xs = TranslationTable + { _codonToAminoAcid = fromList [ (t^.baseCodon, t) | t ← xs ] + , _aminoAcidtoCodons = fromListWith (++) [ (t^.aminoAcid, [t]) | t ← xs ] + , _tableID = i + , _tableName = hdr + } + diff --git a/BiobaseENA.cabal b/BiobaseENA.cabal new file mode 100644 --- /dev/null +++ b/BiobaseENA.cabal @@ -0,0 +1,94 @@ +Cabal-version: 2.2 +Name: BiobaseENA +Version: 0.0.0.1 +License: BSD-3-Clause +License-file: LICENSE +Author: Christian Hoener zu Siederdissen +Maintainer: choener@bioinf.uni-leipzig.de +Copyright: Christian Hoener zu Siederdissen, 2019 +homepage: https://github.com/choener/BiobaseENA +bug-reports: https://github.com/choener/BiobaseENA/issues +Stability: Experimental +Category: Data +Build-type: Simple +tested-with: GHC == 8.4.4 +Synopsis: European Nucleotide Archive data +Description: + Provides data (and later API) access to the European Nucleotide Archive. + . + * Taxonomy Service / Translation tables (hardcoded) + + + +extra-source-files: + changelog.md + README.md + sources/translation-tables + + +common deps + build-depends: base >= 4.7 && < 5.0 + , bytestring + , containers + , directory + , file-embed >= 0.0.10 + , lens >= 4.0 + , megaparsec >= 7.0 + , mtl >= 2.0 + , text + , vector >= 0.10 + , vector-th-unbox >= 0.2 + -- + , BiobaseTypes == 0.2.0.* + ghc-options: + -O2 + -funbox-strict-fields + default-language: + Haskell2010 + default-extensions: BangPatterns + , FlexibleContexts + , FlexibleInstances + , MultiWayIf + , LambdaCase + , OverloadedStrings + , TemplateHaskell + , TypeFamilies + , UnicodeSyntax + + +library + import: + deps + exposed-modules: + Biobase.GeneticCodes + Biobase.GeneticCodes.Embedded + Biobase.GeneticCodes.Import + Biobase.GeneticCodes.Translation + Biobase.GeneticCodes.Types + + + + +test-suite properties + import: + deps + type: + exitcode-stdio-1.0 + main-is: + properties.hs + ghc-options: + -threaded -rtsopts -with-rtsopts=-N + hs-source-dirs: + tests + build-depends: BiobaseENA + , QuickCheck >= 2.7 + , tasty >= 0.11 + , tasty-quickcheck >= 0.8 + , tasty-th >= 0.1 + + + +source-repository head + type: git + location: git://github.com/choener/BiobaseENA + diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,30 @@ +Copyright Christian Hoener zu Siederdissen 2018 + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + + * Neither the name of Christian Hoener zu Siederdissen nor the names of other + contributors may be used to endorse or promote products derived + from this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS +"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT +LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR +A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT +OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT +LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, +DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,16 @@ +[![Build Status](https://travis-ci.org/choener/BiobaseENA.svg?branch=master)](https://travis-ci.org/choener/BiobaseENA) + +# BiobaseENA + +Data from the European Nucleotide Archive. Currently only provides translation +table but is supposed to, at some point, provide API access to their data. + + + +#### Contact + +Christian Hoener zu Siederdissen +Leipzig University, Leipzig, Germany +choener@bioinf.uni-leipzig.de +http://www.bioinf.uni-leipzig.de/~choener/ + diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,2 @@ +import Distribution.Simple +main = defaultMain diff --git a/changelog.md b/changelog.md new file mode 100644 --- /dev/null +++ b/changelog.md @@ -0,0 +1,6 @@ +0.0.0.1 +------- + +- initial creation +- using megaparsec (testing for now) + diff --git a/sources/translation-tables b/sources/translation-tables new file mode 100644 --- /dev/null +++ b/sources/translation-tables @@ -0,0 +1,125 @@ +1: Standard +Amino acids FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons ---M---------------M---------------M---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +2: Vertebrate Mitochondrial +Amino acids FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG +Start codons --------------------------------MMMM---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +3: Yeast Mitochondrial +Amino acids FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons ----------------------------------MM---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +4: Mold Mitochondrial; Protozoan Mitochondrial; Coelenterate Mitochondrial; Mycoplasma; Spiroplasma +Amino acids FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons --MM---------------M------------MMMM---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +5: Invertebrate Mitochondrial +Amino acids FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG +Start codons ---M----------------------------MMMM---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +6: Ciliate Nuclear; Dasycladacean Nuclear; Hexamita Nuclear +Amino acids FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons -----------------------------------M---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +9: Echinoderm Mitochondrial; Flatworm Mitochondrial +Amino acids FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG +Start codons -----------------------------------M---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +10: Euplotid Nuclear +Amino acids FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons -----------------------------------M---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +11: Bacterial, Archaeal and Plant Plastid +Amino acids FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons ---M---------------M------------MMMM---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +12: Alternative Yeast Nuclear +Amino acids FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons -------------------M---------------M---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +13: Ascidian Mitochondrial +Amino acids FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG +Start codons ---M------------------------------MM---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +14: Alternative Flatworm Mitochondrial +Amino acids FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG +Start codons -----------------------------------M---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +16: Chlorophycean Mitochondrial +Amino acids FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons -----------------------------------M---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +21: Trematode Mitochondrial +Amino acids FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG +Start codons -----------------------------------M---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +22: Scenedesmus obliquus mitochondrial +Amino acids FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons -----------------------------------M---------------------------- +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +23: Thraustochytrium mitochondrial code +Amino acids FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons --------------------------------M--M---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +24: Pterobranchia Mitochondrial +Amino acids FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSSKVVVVAAAADDEEGGGG +Start codons ---M---------------M---------------M---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG + +25: Candidate Division SR1 and Gracilibacteria +Amino acids FFLLSSSSYY**CCGWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG +Start codons ---M-------------------------------M---------------M------------ +Base 1 TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG +Base 2 TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG +Base 3 TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG diff --git a/tests/properties.hs b/tests/properties.hs new file mode 100644 --- /dev/null +++ b/tests/properties.hs @@ -0,0 +1,8 @@ + +module Main where + + + +main ∷ IO () +main = return () +