cobot-io 0.1.3.13 → 0.1.3.14

raw patch · 8 files changed

+372/−41 lines, 8 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 +11/−9
• src/Bio/FASTA/Parser.hs +118/−9
• src/Bio/FASTA/Type.hs +203/−5
• src/Bio/FASTA/Writer.hs +23/−12
• test/FastaParserSpec.hs +10/−3
• test/FastaWriterSpec.hs +1/−1

@@ -2,6 +2,10 @@  ## [Unreleased] +## [0.1.3.14] - 2021-02-10+### Changed+- Added ability to parse modifications in Fasta.+ ## [0.1.3.13] - 2021-01-02 ### Changed - Allow `QuickCheck-2.14`.

@@ -4,10 +4,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 9dde2f0490e3c7f6e31e47e18e9de44a3d87d607b09a62b6d723471fffc2f0a5+-- hash: b4805dfc259e39022dd3313837d29888036016ead10be1b3b52215e16a76f7a7  name:           cobot-io-version:        0.1.3.13+version:        0.1.3.14 synopsis:       Biological data file formats and IO description:    Please see the README on GitHub at <https://github.com/biocad/cobot-io#readme> category:       Bio

@@ -2,24 +2,26 @@  module Bio.FASTA   ( module T+  , WritableFastaToken (..)   , fromFile   , toFile   , fastaP   , fastaPGeneric   ) 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 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)+import Control.Monad.Fail (MonadFail (..))+import Prelude            hiding (fail, readFile, writeFile) #else-import           Prelude                hiding (readFile, writeFile)+import Prelude hiding (readFile, writeFile) #endif++import Bio.FASTA.Parser+import Bio.FASTA.Type   as T+import Bio.FASTA.Writer (WritableFastaToken (..), fastaToText)  -- | Reads 'FastaSequence' from given file. --

@@ -1,35 +1,46 @@+{-# OPTIONS_GHC -fno-warn-orphans #-}+ module Bio.FASTA.Parser   ( fastaP   , fastaPGeneric   ) where -import Bio.FASTA.Type       (Fasta, FastaItem (..))+import Bio.FASTA.Type       (Fasta, FastaItem (..), ModItem (..), Modification (..),+                             ParsableFastaToken (..)) import Bio.Sequence         (BareSequence, bareSequence)+import Control.Applicative  ((<|>)) import Data.Attoparsec.Text (Parser, char, choice, endOfInput, endOfLine, many', many1', satisfy,-                             skipWhile, takeWhile)-import Data.Char            (isLetter, isSpace)+                             skipWhile, string, takeWhile, try)+import Data.Char            (isAlphaNum, isLetter, isSpace) import Data.Text            (Text, strip) import Prelude              hiding (takeWhile) +instance ParsableFastaToken Char where+    parseToken = satisfy++instance ParsableFastaToken ModItem where+    parseToken predicate = (Mod <$> modificationP) <|> (Letter <$> satisfy predicate)++ -- | Parser of .fasta file. ---fastaP :: Parser (Fasta Char)+fastaP :: ParsableFastaToken a => Parser (Fasta a) fastaP = fastaPGeneric isLetter -fastaPGeneric :: (Char -> Bool) -> Parser (Fasta Char)+fastaPGeneric :: ParsableFastaToken a => (Char -> Bool) -> Parser (Fasta a) fastaPGeneric = many' . item -item :: (Char -> Bool) -> Parser (FastaItem Char)+item :: ParsableFastaToken a => (Char -> Bool) -> Parser (FastaItem a) item predicate = (FastaItem <$> seqName <*> fastaSeq predicate) <* skipWhile isSpace  seqName :: Parser Text seqName = strip <$> (char '>' *> tabs *> takeWhile (`notElem` ['\n', '\r']) <* tabs <* eol) -fastaSeq :: (Char -> Bool) -> Parser (BareSequence Char)+fastaSeq :: ParsableFastaToken a => (Char -> Bool) -> Parser (BareSequence a) fastaSeq predicate = bareSequence . mconcat <$> many' (line predicate) -line :: (Char -> Bool) -> Parser String-line predicate = concat <$> many1' (many1' (satisfy predicate) <* many' (char ' ')) <* eol+line :: ParsableFastaToken a => (Char -> Bool) -> Parser [a]+line predicate = concat <$> many1' (many1' (parseToken predicate) <* many' (char ' ')) <* eol  eol :: Parser () eol = tabs *> choice [slashN, endOfInput]@@ -39,3 +50,101 @@  tabs :: Parser () tabs = () <$ many' (char '\t')++modificationP :: Parser Modification+modificationP +  =   string "[A*]" *> pure Mod_A_Star+  <|> string "[C*]" *> pure Mod_C_Star+  <|> string "[G*]" *> pure Mod_G_Star+  <|> string "[T*]" *> pure Mod_T_Star+  <|> string "[rA]" *> pure Mod_rA+  <|> string "[rC]" *> pure Mod_rC+  <|> string "[rG]" *> pure Mod_rG+  <|> string "[rU]" *> pure Mod_rU+  <|> string "[+A]" *> pure Mod_Plus_A+  <|> string "[+C]" *> pure Mod_Plus_C+  <|> string "[+G]" *> pure Mod_Plus_G+  <|> string "[+T]" *> pure Mod_Plus_T+  <|> string "[rAf]" *> pure Mod_rAf+  <|> string "[rCf]" *> pure Mod_rCf+  <|> string "[rGf]" *> pure Mod_rGf+  <|> string "[rUf]" *> pure Mod_rUf+  <|> string "[mA]" *> pure Mod_mA+  <|> string "[mC]" *> pure Mod_mC+  <|> string "[mG]" *> pure Mod_mG+  <|> string "[mU]" *> pure Mod_mU+  <|> string "[mA*]" *> pure Mod_mA_Star+  <|> string "[mC*]" *> pure Mod_mC_Star+  <|> string "[mG*]" *> pure Mod_mG_Star+  <|> string "[mU*]" *> pure Mod_mU_Star+  <|> string "[dU]" *> pure Mod_dU+  <|> string "[5Bio]" *> pure Mod_5Bio+  <|> string "[iBio]" *> pure Mod_iBio+  <|> string "[56FAM]" *> pure Mod_56FAM+  <|> string "[36FAM]" *> pure Mod_36FAM+  <|> string "[5HEX]" *> pure Mod_5HEX+  <|> string "[5TMR]" *> pure Mod_5TMR+  <|> string "[3BHQ1]" *> pure Mod_3BHQ1+  <|> string "[3BHQ2]" *> pure Mod_3BHQ2+  <|> string "[5NH2]" *> pure Mod_5NH2+  <|> string "[3NH2]" *> pure Mod_3NH2+  <|> string "[5PO4]" *> pure Mod_5PO4+  <|> string "[3PO4]" *> pure Mod_3PO4+  <|> string "[3BioTEG]" *> pure Mod_3BioTEG+  <|> string "[C12]" *> pure Mod_C12+  <|> string "[NHSdT]" *> pure Mod_NHSdT+  <|> string "[5Mal]" *> pure Mod_5Mal+  <|> string "[5thio]" *> pure Mod_5thio+  <|> string "[3thio]" *> pure Mod_3thio+  <|> string "[3azide]" *> pure Mod_3azide+  <|> string "[3alkine]" *> pure Mod_3alkine+  <|> string "[5CholTEG]" *> pure Mod_5CholTEG+  <|> string "[3CholTEG]" *> pure Mod_3CholTEG+  <|> string "[5C10]" *> pure Mod_5C10+  <|> string "[5Alk]" *> pure Mod_5Alk+  <|> string "[GC]" *> pure Mod_GC+  <|> string "[GT]" *> pure Mod_GT+  <|> string "[AT]" *> pure Mod_AT+  <|> string "[TG]" *> pure Mod_TG+  <|> string "[AC]" *> pure Mod_AC+  <|> string "[CC]" *> pure Mod_CC+  <|> string "[AA]" *> pure Mod_AA+  <|> string "[TC]" *> pure Mod_TC+  <|> string "[TT]" *> pure Mod_TT+  <|> string "[CG]" *> pure Mod_CG+  <|> string "[GG]" *> pure Mod_GG+  <|> string "[AG]" *> pure Mod_AG+  <|> string "[GA]" *> pure Mod_GA+  <|> string "[CA]" *> pure Mod_CA+  <|> string "[CT]" *> pure Mod_CT+  <|> string "[TA]" *> pure Mod_TA+  <|> string "[AAA]" *> pure Mod_AAA+  <|> string "[AAC]" *> pure Mod_AAC+  <|> string "[ACT]" *> pure Mod_ACT+  <|> string "[ATC]" *> pure Mod_ATC+  <|> string "[ATG]" *> pure Mod_ATG+  <|> string "[CAG]" *> pure Mod_CAG+  <|> string "[AGA]" *> pure Mod_AGA+  <|> string "[CAT]" *> pure Mod_CAT+  <|> string "[CCG]" *> pure Mod_CCG+  <|> string "[CGT]" *> pure Mod_CGT+  <|> string "[CTG]" *> pure Mod_CTG+  <|> string "[GAA]" *> pure Mod_GAA+  <|> string "[GAC]" *> pure Mod_GAC+  <|> string "[GCT]" *> pure Mod_GCT+  <|> string "[GGT]" *> pure Mod_GGT+  <|> string "[GTT]" *> pure Mod_GTT+  <|> string "[TAC]" *> pure Mod_TAC+  <|> string "[TCT]" *> pure Mod_TCT+  <|> string "[TGC]" *> pure Mod_TGC+  <|> string "[TGG]" *> pure Mod_TGG+  <|> string "[TTC]" *> pure Mod_TTC+  <|> string "[TTT]" *> pure Mod_TTT+  <|> unknownP++unknownP :: Parser Modification+unknownP = try $ do+    _ <- char '[' +    m <- many1' $ satisfy (\c -> isAlphaNum c || c `elem` ['+', '-', '*', '_'])+    _ <- char ']'+    pure $ Unknown ("[" <> m <> "]")

@@ -1,10 +1,15 @@ module Bio.FASTA.Type   ( Fasta   , FastaItem (..)+  , ParsableFastaToken (..)+  , Modification (..)+  , ModItem (..)+  , modificationToString   ) where -import           Bio.Sequence (BareSequence)-import           Data.Text    (Text)+import Bio.Sequence         (BareSequence)+import Data.Attoparsec.Text (Parser)+import Data.Text            (Text)  -- | Type alias for FASTA file. --  satisfies the following format : >(\s|\t)*[^\n\r]+(\s|\t)*(\n|\r)*((\w|\s)(\n|\r)*)*@@ -14,7 +19,200 @@ -- | One record in FASTA file. -- data FastaItem a-   = FastaItem { name :: Text           -- ^ name of the sequence-               , sequ :: BareSequence a -- ^ bare sequence-               }+  = FastaItem+      { name :: Text+        -- ^ name of the sequence+      , sequ :: BareSequence a+        -- ^ bare sequence+      }   deriving (Eq, Show, Functor)++class ParsableFastaToken a where+    parseToken :: (Char -> Bool) -> Parser a++data ModItem+  = Mod Modification+  | Letter Char+  deriving (Eq, Show)++data Modification+  = Mod_A_Star+  | Mod_C_Star+  | Mod_G_Star+  | Mod_T_Star+  | Mod_rA+  | Mod_rC+  | Mod_rG+  | Mod_rU+  | Mod_Plus_A+  | Mod_Plus_C+  | Mod_Plus_G+  | Mod_Plus_T+  | Mod_rAf+  | Mod_rCf+  | Mod_rGf+  | Mod_rUf+  | Mod_mA+  | Mod_mC+  | Mod_mG+  | Mod_mU+  | Mod_mA_Star+  | Mod_mC_Star+  | Mod_mG_Star+  | Mod_mU_Star+  | Mod_dU+  | Mod_5Bio+  | Mod_iBio+  | Mod_56FAM+  | Mod_36FAM+  | Mod_5HEX+  | Mod_5TMR+  | Mod_3BHQ1+  | Mod_3BHQ2+  | Mod_5NH2+  | Mod_3NH2+  | Mod_5PO4+  | Mod_3PO4+  | Mod_3BioTEG+  | Mod_C12+  | Mod_NHSdT+  | Mod_5Mal+  | Mod_5thio+  | Mod_3thio+  | Mod_3azide+  | Mod_3alkine+  | Mod_5CholTEG+  | Mod_3CholTEG+  | Mod_5C10+  | Mod_5Alk+  | Mod_GC+  | Mod_GT+  | Mod_AT+  | Mod_TG+  | Mod_AC+  | Mod_CC+  | Mod_AA+  | Mod_TC+  | Mod_TT+  | Mod_CG+  | Mod_GG+  | Mod_AG+  | Mod_GA+  | Mod_CA+  | Mod_CT+  | Mod_TA+  | Mod_AAA+  | Mod_AAC+  | Mod_ACT+  | Mod_ATC+  | Mod_ATG+  | Mod_CAG+  | Mod_AGA+  | Mod_CAT+  | Mod_CCG+  | Mod_CGT+  | Mod_CTG+  | Mod_GAA+  | Mod_GAC+  | Mod_GCT+  | Mod_GGT+  | Mod_GTT+  | Mod_TAC+  | Mod_TCT+  | Mod_TGC+  | Mod_TGG+  | Mod_TTC+  | Mod_TTT+  | Unknown String+  deriving (Eq, Show)++modificationToString :: Modification -> String+modificationToString Mod_A_Star   = "[A*]"+modificationToString Mod_C_Star   = "[C*]"+modificationToString Mod_G_Star   = "[G*]"+modificationToString Mod_T_Star   = "[T*]"+modificationToString Mod_rA       = "[rA]"+modificationToString Mod_rC       = "[rC]"+modificationToString Mod_rG       = "[rG]"+modificationToString Mod_rU       = "[rU]"+modificationToString Mod_Plus_A   = "[+A]"+modificationToString Mod_Plus_C   = "[+C]"+modificationToString Mod_Plus_G   = "[+G]"+modificationToString Mod_Plus_T   = "[+T]"+modificationToString Mod_rAf      = "[rAf]"+modificationToString Mod_rCf      = "[rCf]"+modificationToString Mod_rGf      = "[rGf]"+modificationToString Mod_rUf      = "[rUf]"+modificationToString Mod_mA       = "[mA]"+modificationToString Mod_mC       = "[mC]"+modificationToString Mod_mG       = "[mG]"+modificationToString Mod_mU       = "[mU]"+modificationToString Mod_mA_Star  = "[mA*]"+modificationToString Mod_mC_Star  = "[mC*]"+modificationToString Mod_mG_Star  = "[mG*]"+modificationToString Mod_mU_Star  = "[mU*]"+modificationToString Mod_dU       = "[dU]"+modificationToString Mod_5Bio     = "[5Bio]"+modificationToString Mod_iBio     = "[iBio]"+modificationToString Mod_56FAM    = "[56FAM]"+modificationToString Mod_36FAM    = "[36FAM]"+modificationToString Mod_5HEX     = "[5HEX]"+modificationToString Mod_5TMR     = "[5TMR]"+modificationToString Mod_3BHQ1    = "[3BHQ1]"+modificationToString Mod_3BHQ2    = "[3BHQ2]"+modificationToString Mod_5NH2     = "[5NH2]"+modificationToString Mod_3NH2     = "[3NH2]"+modificationToString Mod_5PO4     = "[5PO4]"+modificationToString Mod_3PO4     = "[3PO4]"+modificationToString Mod_3BioTEG  = "[3BioTEG]"+modificationToString Mod_C12      = "[C12]"+modificationToString Mod_NHSdT    = "[NHSdT]"+modificationToString Mod_5Mal     = "[5Mal]"+modificationToString Mod_5thio    = "[5thio]"+modificationToString Mod_3thio    = "[3thio]"+modificationToString Mod_3azide   = "[3azide]"+modificationToString Mod_3alkine  = "[3alkine]"+modificationToString Mod_5CholTEG = "[5CholTEG]"+modificationToString Mod_3CholTEG = "[3CholTEG]"+modificationToString Mod_5C10     = "[5C10]"+modificationToString Mod_5Alk     = "[5Alk]"+modificationToString Mod_GC       = "[GC]"+modificationToString Mod_GT       = "[GT]"+modificationToString Mod_AT       = "[AT]"+modificationToString Mod_TG       = "[TG]"+modificationToString Mod_AC       = "[AC]"+modificationToString Mod_CC       = "[CC]"+modificationToString Mod_AA       = "[AA]"+modificationToString Mod_TC       = "[TC]"+modificationToString Mod_TT       = "[TT]"+modificationToString Mod_CG       = "[CG]"+modificationToString Mod_GG       = "[GG]"+modificationToString Mod_AG       = "[AG]"+modificationToString Mod_GA       = "[GA]"+modificationToString Mod_CA       = "[CA]"+modificationToString Mod_CT       = "[CT]"+modificationToString Mod_TA       = "[TA]"+modificationToString Mod_AAA      = "[AAA]"+modificationToString Mod_AAC      = "[AAC]"+modificationToString Mod_ACT      = "[ACT]"+modificationToString Mod_ATC      = "[ATC]"+modificationToString Mod_ATG      = "[ATG]"+modificationToString Mod_CAG      = "[CAG]"+modificationToString Mod_AGA      = "[AGA]"+modificationToString Mod_CAT      = "[CAT]"+modificationToString Mod_CCG      = "[CCG]"+modificationToString Mod_CGT      = "[CGT]"+modificationToString Mod_CTG      = "[CTG]"+modificationToString Mod_GAA      = "[GAA]"+modificationToString Mod_GAC      = "[GAC]"+modificationToString Mod_GCT      = "[GCT]"+modificationToString Mod_GGT      = "[GGT]"+modificationToString Mod_GTT      = "[GTT]"+modificationToString Mod_TAC      = "[TAC]"+modificationToString Mod_TCT      = "[TCT]"+modificationToString Mod_TGC      = "[TGC]"+modificationToString Mod_TGG      = "[TGG]"+modificationToString Mod_TTC      = "[TTC]"+modificationToString Mod_TTT      = "[TTT]"+modificationToString (Unknown s)  = s+

@@ -1,23 +1,34 @@ module Bio.FASTA.Writer   ( fastaToText+  , WritableFastaToken (..)   ) where -import           Bio.FASTA.Type     (Fasta, FastaItem(..))-import           Bio.Sequence       (BareSequence, sequ)-import           Control.Lens       ((^.))-import           Data.Text          (Text, pack)-import           Data.List.Split    (chunksOf)-import           Data.Vector        (Vector, toList)-import           Prelude     hiding (drop)+import Bio.FASTA.Type  (Fasta, FastaItem (..), ModItem (..), modificationToString)+import Bio.Sequence    (BareSequence, sequ)+import Control.Lens    ((^.))+import Data.List.Split (chunksOf)+import Data.Text       (Text, pack)+import Data.Vector     (Vector, toList)+import Prelude         hiding (drop) -fastaToText :: Fasta Char -> Text+class WritableFastaToken a where+    tokenToString :: a -> String++instance WritableFastaToken Char where+    tokenToString = pure++instance WritableFastaToken ModItem where+    tokenToString (Letter l) = [l]+    tokenToString (Mod m)    = modificationToString m++fastaToText :: WritableFastaToken a => Fasta a -> Text fastaToText f = mconcat $ map writeItem f -writeItem :: FastaItem Char -> Text+writeItem :: WritableFastaToken a => FastaItem a -> Text writeItem (FastaItem name s) = ">" <> name <> "\n" <> seq2Text s -seq2Text :: BareSequence Char -> Text+seq2Text :: WritableFastaToken a => BareSequence a -> Text seq2Text s = pack $ vector2Text $ s ^. Bio.Sequence.sequ -vector2Text :: Vector Char -> String-vector2Text v = concatMap (++ "\n") $ chunksOf 80 $ toList v+vector2Text :: WritableFastaToken a => Vector a -> String+vector2Text v = concatMap (++ "\n") $ chunksOf 80 $ concatMap tokenToString $ toList v

@@ -3,7 +3,7 @@ module FastaParserSpec where  import           Bio.FASTA.Parser     (fastaP)-import           Bio.FASTA.Type       (Fasta, FastaItem (..))+import           Bio.FASTA.Type       (Fasta, FastaItem (..), ModItem (..), Modification (..)) import           Bio.Sequence         (bareSequence) import           Data.Attoparsec.Text (endOfInput, parseOnly) import           Data.Text            (Text)@@ -23,13 +23,14 @@     sequenceWithSeveralEndOfLineInSequence     sequenceWithTabsInName     sequenceWithTabsInSequence+    sequenceWithModifications     toughParserTests  emptyFasta :: Spec emptyFasta = describe "emptyFasta" $ do     it "correctly parses empty fasta" $ do         let res = parseOnly fastaP ""-        res `shouldBe` Right []+        res `shouldBe` Right ([] :: Fasta Char)  onlyName :: Spec onlyName = describe "onlyName" $ do@@ -59,7 +60,7 @@ sequenceWithWrongName = describe "sequenceWithWrongName" $ do     it "correctly parses incorrect sequence with wrong name" $ do         let res = parseOnly fastaP "123\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE"-        res `shouldBe` Right []+        res `shouldBe` Right ([] :: Fasta Char)  sequenceWithSpacesInName :: Spec sequenceWithSpacesInName = describe "sequenceWithSpacesInName" $ do@@ -90,6 +91,12 @@     it "correctly parses sequence with tabs between sequence parts" $ do         let res = parseOnly fastaP ">this is my sequence\nIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSE\t\t\nYYYYYYYYYYYYYYYYYYYYYYYY\t\n"         res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence "IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEGITWTLDQSSEYYYYYYYYYYYYYYYYYYYYYYYY")]++sequenceWithModifications :: Spec+sequenceWithModifications = describe "sequenceWithModifications" $ do+    it "correctly parses sequence with modifications" $ do+        let res = parseOnly fastaP ">this is my sequence\nIWEL[mU*]KKDVYV\t\t\nYY[56FAM]YY[Trololo]YY\t\n"+        res `shouldBe` Right [FastaItem "this is my sequence" (bareSequence [Letter 'I', Letter 'W', Letter 'E', Letter 'L', Mod Mod_mU_Star, Letter 'K', Letter 'K', Letter 'D', Letter 'V', Letter 'Y', Letter 'V', Letter 'Y', Letter 'Y', Mod Mod_56FAM, Letter 'Y', Letter 'Y', Mod (Unknown "[Trololo]"), Letter 'Y', Letter 'Y'])]  toughParserTests :: Spec toughParserTests = describe "various parser tests" $ do

@@ -15,7 +15,7 @@ emptyFasta :: Spec emptyFasta = describe "emptyFasta" $ do     it "correctly write empty fasta" $ do-        let res = fastaToText []+        let res = fastaToText ([] :: [FastaItem Char])         res `shouldBe` ""  oneShortSequence :: Spec