cobot-io 0.1.2.6 → 0.1.2.7

raw patch · 10 files changed

+88/−40 lines, 10 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ChangeLog.md +4/−0
• cobot-io.cabal +2/−2
• src/Bio/FASTA.hs +14/−7
• src/Bio/GB.hs +7/−1
• src/Bio/MAE.hs +6/−1
• src/Bio/MMTF.hs +8/−2
• src/Bio/MMTF/Decode.hs +10/−10
• src/Bio/MMTF/Decode/Codec.hs +8/−2
• src/Bio/MMTF/Decode/MessagePack.hs +22/−14
• src/Bio/Uniprot.hs +7/−1

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.2.7] - 2020-02-11+### Changed+- Support GHC-8.8.+ ## [0.1.2.6] - 2019-12-12 ### Fixed - Fixes for instance of `StructureModels` for `Mae` when working with structures without explicit chain names.

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 0f03c19b37ba0793d464c62245414745d11715571fb56535d09dedf96fc5f683+-- hash: b98bae8044cc69e013da5d57a2077a7d9b4f9330def6ecd281f524600c734fa9  name:           cobot-io-version:        0.1.2.6+version:        0.1.2.7 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/less-wrong/cobot-io#readme> category:       Bio

@@ -1,3 +1,5 @@+{-# LANGUAGE CPP #-}+ module Bio.FASTA   ( module T   , fromFile@@ -6,16 +8,21 @@   ) where  import           Bio.FASTA.Parser-import           Bio.FASTA.Type             as T-import           Bio.FASTA.Writer           (fastaToText)-import           Control.Monad.IO.Class     (MonadIO, liftIO)-import           Data.Attoparsec.Text       (parseOnly)-import           Data.Text.IO               (readFile, writeFile)-import           Prelude            hiding  (writeFile, readFile)+import           Bio.FASTA.Type         as T+import           Bio.FASTA.Writer       (fastaToText)+import           Control.Monad.IO.Class (MonadIO, liftIO)+import           Data.Attoparsec.Text   (parseOnly)+import           Data.Text.IO           (readFile, writeFile)+#if !MIN_VERSION_base(4,13,0)+import           Control.Monad.Fail     (MonadFail (..))+import           Prelude                hiding (fail, readFile, writeFile)+#else+import           Prelude                hiding (readFile, writeFile)+#endif  -- | Reads 'FastaSequence' from given file. ---fromFile :: MonadIO m => FilePath -> m (Fasta Char)+fromFile :: (MonadFail m, MonadIO m) => FilePath -> m (Fasta Char) fromFile f = liftIO (readFile f) >>= either fail pure . parseOnly fastaP  -- | Writes 'FastaSequence' to file.

@@ -1,3 +1,5 @@+{-# LANGUAGE CPP #-}+ module Bio.GB   ( module T   , fromFile@@ -15,10 +17,14 @@ import           Data.Bifunctor         (first) import           Data.Text              (Text, pack) import qualified Data.Text.IO           as TIO (readFile, writeFile)+#if !MIN_VERSION_base(4,13,0)+import           Control.Monad.Fail     (MonadFail(..))+import           Prelude                hiding (fail)+#endif  -- | Reads 'GenBankSequence' from givem file. ---fromFile :: MonadIO m => FilePath -> m GenBankSequence+fromFile :: (MonadFail m, MonadIO m) => FilePath -> m GenBankSequence fromFile f = liftIO (TIO.readFile f) >>= either fail pure . parseOnly genBankP  -- | Writes 'GenBankSequence' to file.

@@ -1,3 +1,4 @@+{-# LANGUAGE CPP #-} {-# LANGUAGE AllowAmbiguousTypes #-} {-# OPTIONS_GHC -fno-warn-orphans #-} @@ -34,10 +35,14 @@ import           Data.Vector            (Vector) import qualified Data.Vector            as V (fromList) import           Linear.V3              (V3 (..))+#if !MIN_VERSION_base(4,13,0)+import           Control.Monad.Fail     (MonadFail(..))+import           Prelude                hiding (fail)+#endif  -- | Reads 'Mae' from givem file. ---fromFile :: MonadIO m => FilePath -> m Mae+fromFile :: (MonadFail m, MonadIO m) => FilePath -> m Mae fromFile f = liftIO (TIO.readFile f) >>= either fail pure . parseOnly maeP  -- | Reads 'Mae' from 'Text'.

@@ -1,3 +1,5 @@+{-# LANGUAGE CPP #-}+ {-# OPTIONS_GHC -fno-warn-orphans #-} module Bio.MMTF   ( module Bio.MMTF.Type@@ -22,14 +24,18 @@ import           Data.Vector            (Vector, empty, toList, (!)) import           Linear.V3              (V3 (..)) import           Network.HTTP.Simple    (getResponseBody, httpLBS)+#if !MIN_VERSION_base(4,13,0)+import           Control.Monad.Fail     (MonadFail(..))+import           Prelude                hiding (fail)+#endif  -- | Decodes a 'ByteString' to 'MMTF' ---decode :: Monad m => ByteString -> m MMTF+decode :: MonadFail m => ByteString -> m MMTF decode = unpack  -- | Fetches MMTF structure from RSCB-fetch :: MonadIO m => String -> m MMTF+fetch :: (MonadFail m, MonadIO m) => String -> m MMTF fetch pdbid = do let url = fromString $ "https://mmtf.rcsb.org/v1.0/full/" <> pdbid                  resp <- httpLBS url                  decode (getResponseBody resp)

@@ -14,19 +14,19 @@  -- | Parses format data from ObjectMap ---formatData :: Monad m => Map Text Object -> m FormatData+formatData :: MonadFail m => Map Text Object -> m FormatData formatData mp = do v <- atP mp "mmtfVersion"  asStr                    p <- atP mp "mmtfProducer" asStr                    pure $ FormatData v p  -- | Parses model data from ObjectMap ---modelData :: Monad m => Map Text Object -> m ModelData+modelData :: MonadFail m => Map Text Object -> m ModelData modelData mp = ModelData . l2v <$> atP mp "chainsPerModel" asIntList  -- | Parses chain data from ObjectMap ---chainData :: Monad m => Map Text Object -> m ChainData+chainData :: MonadFail m => Map Text Object -> m ChainData chainData mp = do gpc <- atP mp "groupsPerChain" asIntList                   cil <- codec5 . parseBinary <$> atP   mp "chainIdList"   asBinary                   cnl <- codec5 . parseBinary <$> atPMD mp "chainNameList" asBinary empty@@ -34,7 +34,7 @@  -- | Parses atom data from ObjectMap ---atomData :: Monad m => Map Text Object -> m AtomData+atomData :: MonadFail m => Map Text Object -> m AtomData atomData mp = do ail' <-       codec8 . parseBinary <$> atPMD mp "atomIdList"    asBinary empty                  all' <- c2s . codec6 . parseBinary <$> atPMD mp "altLocList"    asBinary empty                  bfl' <-      codec10 . parseBinary <$> atPMD mp "bFactorList"   asBinary empty@@ -46,7 +46,7 @@  -- | Parses group data from ObjectMap ---groupData :: Monad m => Map Text Object -> m GroupData+groupData :: MonadFail m => Map Text Object -> m GroupData groupData mp = do gl' <-                                        atP   mp "groupList"          asObjectList >>= traverse (transformObjectMap >=> groupType)                   gtl' <-              codec4 . parseBinary <$> atP   mp "groupTypeList"     asBinary                   gil' <-              codec8 . parseBinary <$> atP   mp "groupIdList"       asBinary@@ -57,7 +57,7 @@  -- | Parses group type from ObjectMap ---groupType :: Monad m => Map Text Object -> m GroupType+groupType :: MonadFail m => Map Text Object -> m GroupType groupType mp = do fcl' <-          atP mp "formalChargeList" asIntList                   anl' <-          atP mp "atomNameList"     asStrList                   el'  <-          atP mp "elementList"      asStrList@@ -70,7 +70,7 @@  -- | Parses structure data from ObjectMap ---structureData :: Monad m => Map Text Object -> m StructureData+structureData :: MonadFail m => Map Text Object -> m StructureData structureData mp = do ttl' <-                                  atPMD mp "title"               asStr        ""                       sid' <-                                  atPMD mp "structureId"         asStr        ""                       dd'  <-                                  atPMD mp "depositionDate"      asStr        ""@@ -98,21 +98,21 @@  -- | Parses bio assembly data from ObjectMap ---bioAssembly :: Monad m => Map Text Object -> m Assembly+bioAssembly :: MonadFail m => Map Text Object -> m Assembly bioAssembly mp = do nme' <- atP mp "name"          asStr                     tlt' <- atP mp "transformList" asObjectList >>= traverse (transformObjectMap >=> transform)                     pure $ Assembly (l2v tlt') nme'  -- | Parses transform data from ObjectMap ---transform :: Monad m => Map Text Object -> m Transform+transform :: MonadFail m => Map Text Object -> m Transform transform mp = do cil' <- atP mp "chainIndexList" asIntList                   mtx' <- atP mp "matrix"         asFloatList >>= m44Dec                   pure $ Transform (l2v cil') mtx'  -- | Parses entity data from ObjectMap ---entity :: Monad m => Map Text Object -> m Entity+entity :: MonadFail m => Map Text Object -> m Entity entity mp = do cil' <- atP mp "chainIndexList" asIntList                dsc' <- atP mp "description"    asStr                tpe' <- atP mp "type"           asStr

@@ -1,3 +1,5 @@+{-# LANGUAGE CPP #-}+ module Bio.MMTF.Decode.Codec where  import           Data.Binary          (Binary, decode)@@ -9,6 +11,10 @@ import           Data.Text            (Text) import qualified Data.Text            as T (pack) +#if !MIN_VERSION_base(4,13,0)+import Bio.MMTF.Decode.MessagePack (MonadFail)+#endif+ import           Bio.MMTF.Type import           Bio.Structure @@ -161,11 +167,11 @@         | n == 7    = Coil         | otherwise = Undefined -ucDec :: Monad m => [Float] -> m UnitCell+ucDec :: MonadFail m => [Float] -> m UnitCell ucDec [a,b,c,d,e,f] = pure $ UnitCell a b c d e f ucDec _             = fail "Wrong list format for unit cell" -m44Dec :: Monad m => [Float] -> m M44+m44Dec :: MonadFail m => [Float] -> m M44 m44Dec [ a11, a12, a13, a14        , a21, a22, a23, a24        , a31, a32, a33, a34

@@ -1,3 +1,5 @@+{-# LANGUAGE CPP #-}+ module Bio.MMTF.Decode.MessagePack where  import           Data.ByteString.Lazy  (ByteString, fromStrict)@@ -8,14 +10,20 @@ import           Data.Text             (Text) import qualified Data.Text             as T (unpack) -transformObjectMap :: Monad m => Object -> m (Map Text Object)-transformObjectMap (ObjectMap kv) = let mkPair :: Monad m => (Object, Object) -> m (Text, Object)+#if !MIN_VERSION_base(4,13,0)+-- Data.MessagePack includes MonadFail constraints only for GHC-8.8+, so we can't use+-- "real" Control.Monad.Fail.MonadFail here on GHC-8.6.+type MonadFail m = Monad m+#endif++transformObjectMap :: MonadFail m => Object -> m (Map Text Object)+transformObjectMap (ObjectMap kv) = let mkPair :: MonadFail m => (Object, Object) -> m (Text, Object)                                         mkPair (ObjectStr txt, v) = pure (txt, v)                                         mkPair _ = fail "Non-string key"                                     in  fromList <$> traverse mkPair kv transformObjectMap _ = fail "Wrong MessagePack MMTF format" -atP :: Monad m => Map Text Object -> Text -> (Text -> Object -> m a) -> m a+atP :: MonadFail m => Map Text Object -> Text -> (Text -> Object -> m a) -> m a atP m k conv =   case M.lookup k m of     Just x  -> conv k x@@ -25,45 +33,45 @@ atPM :: Monad m => Map Text Object -> Text -> (Text -> Object -> m a) -> m (Maybe a) atPM m k conv = traverse (conv k) $ M.lookup k m -atPMD :: Monad m => Map Text Object -> Text -> (Text -> Object -> m a) -> a -> m a+atPMD :: MonadFail m => Map Text Object -> Text -> (Text -> Object -> m a) -> a -> m a atPMD m k conv def = do x <- atPM m k conv                         case x of                           Just r  -> pure r                           Nothing -> pure def-                       -asStr :: Monad m => Text -> Object -> m Text++asStr :: MonadFail m => Text -> Object -> m Text asStr _ (ObjectStr s) = pure s asStr m _             = fail $ T.unpack m <> ": not a string data" -asChar :: Monad m => Text -> Object -> m Char+asChar :: MonadFail m => Text -> Object -> m Char asChar m = (head . T.unpack <$>) . asStr m -asInt :: (Monad m, Integral a) => Text -> Object -> m a+asInt :: (MonadFail m, Integral a) => Text -> Object -> m a asInt _ (ObjectInt i)  = pure (fromIntegral i) asInt _ (ObjectWord w) = pure (fromIntegral w) asInt m _              = fail $ T.unpack m <> ": not an int data" -asFloat :: Monad m => Text -> Object -> m Float+asFloat :: MonadFail m => Text -> Object -> m Float asFloat _ (ObjectFloat  f) = pure f asFloat _ (ObjectDouble f) = pure (realToFrac f) asFloat m _                = fail $ T.unpack m <> ": not a float data" -asIntList :: (Monad m, Integral a) => Text -> Object -> m [a]+asIntList :: (MonadFail m, Integral a) => Text -> Object -> m [a] asIntList m (ObjectArray l) = traverse (asInt m) l asIntList m _               = fail $ T.unpack m <> ": not an array of ints data" -asStrList :: Monad m => Text -> Object -> m [Text]+asStrList :: MonadFail m => Text -> Object -> m [Text] asStrList m (ObjectArray l) = traverse (asStr m) l asStrList m _               = fail $ T.unpack m <> ": not an array of string data" -asFloatList :: Monad m => Text -> Object -> m [Float]+asFloatList :: MonadFail m => Text -> Object -> m [Float] asFloatList m (ObjectArray l) = traverse (asFloat m) l asFloatList m _               = fail $ T.unpack m <> ": not an array of float data" -asObjectList :: Monad m => Text -> Object -> m [Object]+asObjectList :: MonadFail m => Text -> Object -> m [Object] asObjectList _ (ObjectArray l) = pure l asObjectList m _               = fail $ T.unpack m <> ": not an array data" -asBinary :: Monad m => Text -> Object -> m ByteString+asBinary :: MonadFail m => Text -> Object -> m ByteString asBinary _ (ObjectBin bs) = pure (fromStrict bs) asBinary m _              = fail $ T.unpack m <> ": not a binary data"

@@ -1,3 +1,5 @@+{-# LANGUAGE CPP #-}+ module Bio.Uniprot   ( module T   , parseRecord@@ -9,12 +11,16 @@ import           Data.Attoparsec.Text   ( parseOnly ) import           Control.Monad.IO.Class ( MonadIO ) import           Network.HTTP.Simple    ( httpBS, getResponseBody )+#if !MIN_VERSION_base(4,13,0)+import           Control.Monad.Fail     ( MonadFail(..) )+import           Prelude                hiding ( fail )+#endif  import           Bio.Uniprot.Type       as T import           Bio.Uniprot.Parser  -- | Fetches Uniprot record from Uniprot-fetch :: MonadIO m => String -> m Record+fetch :: (MonadFail m, MonadIO m) => String -> m Record fetch recid = do let url = fromString $ "https://www.uniprot.org/uniprot/" <> recid <> ".txt"                  resp <- httpBS url                  case parseOnly parseRecord (decodeUtf8 $ getResponseBody resp) of