uniprot-kb 0.1.0.0 → 0.1.0.1

raw patch · 6 files changed

+67/−37 lines, 6 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ChangeLog.md +5/−0
• README.md +21/−4
• src/Bio/Uniprot/Parser.hs +35/−27
• src/Bio/Uniprot/Type.hs +2/−2
• test/Spec.hs +2/−2
• uniprot-kb.cabal +2/−2

@@ -7,5 +7,10 @@  ## [Unreleased] +## 0.1.0.1+* Small fixes in description fields read+* Documentation fixes+* Usage example in README+ ## 0.1.0.0 * Any UniProt-KB file can be parsed

@@ -15,12 +15,24 @@  ## Usage example -To use the parser and types import:-```-λ> import Bio.Uniprot+You can use this simple code to parse any UniProt file:++``` haskell+import           Bio.Uniprot+import           Data.Attoparsec.Text (parseOnly)+import           Data.Text            (Text)+import qualified Data.Text.IO         as TIO+import           Text.Pretty.Simple   (pPrint)++main :: IO ()+main = do+    uniprot <- TIO.getContents+    case parseOnly parseRecord uniprot of+      Left err  -> putStrLn "Error on parse"+      Right obj -> pPrint obj ``` -Than you can parse any `Text` of UniProt by using `parseRecord` function. The result will be presented by+So you can parse any stdin `Text` of UniProt by using `parseRecord` function. The result will be presented by a `Record` datatype: ``` haskell data Record = Record@@ -42,4 +54,9 @@   , ft   :: [FT]   , sq   :: SQ   } deriving (Show, Eq, Ord)+```++You can run this to test the implementation:+``` bash+stack runhaskell uniprot.hs < example/LOLA2_DROME.dat ```

@@ -3,7 +3,7 @@ {-# LANGUAGE TupleSections     #-} module Bio.Uniprot.Parser where -import           Prelude              hiding (concat, init, null)+import           Prelude              hiding (init, null) import qualified Prelude              as P (concat, id, init)  import           Bio.Uniprot.Type@@ -16,8 +16,6 @@                                        splitOn, unpack, unwords) import           Data.Void -import           Debug.Trace          (trace)- -- |Describes possible name type of DE section. data NameType = RecName | AltName | SubName | Flags | None   deriving (Show)@@ -212,6 +210,7 @@     char '.'     pure OH{..} +-- |Parses RN, RP, RC, RX, RG, RA, RT and RL lines of UniProt-KB text file. parseRef :: Parser Reference parseRef = do     rn <- parseRN@@ -225,7 +224,7 @@     rt <- optional  (parseRT <* endOfLine)     rl <- parseRL     pure Reference{..}-  where    +  where     parseRN :: Parser Int     parseRN = (string "RN   [" *> decimal) <* char ']' @@ -260,6 +259,7 @@         string "RL   "         pack . P.init <$> parseMultiLineComment "RL" 3 +-- |Parses CC lines of UniProt-KB text file. parseCC :: Parser CC parseCC = do     string "CC   -!- "@@ -269,6 +269,7 @@     comment <- pack <$> parseMultiLineComment "CC" 7     pure CC{..} +-- |Parses DR lines of UniProt-KB text file. parseDR :: Parser DR parseDR = do     string "DR   "@@ -327,7 +328,7 @@         splitStr n acc ('(':xs)     = splitStr (n+1) ('(':acc) xs         splitStr n acc (')':xs)     = splitStr (n-1) (')':acc) xs         splitStr n acc (x:xs)       = splitStr n (x:acc) xs-    + -- |Parses SQ lines of UniProt-KB text file. parseSQ :: Parser SQ parseSQ = do@@ -352,28 +353,29 @@  -- |Parses whole UniProt-KB record. parseRecord :: Parser Record-parseRecord = Record <$>          (parseID  <* endOfLine)-                     <*>          (parseAC  <* endOfLine)-                     <*>          (parseDT  <* endOfLine)-                     <*>          (parseDE  <* endOfLine)-                     <*>          (parseGN  <* endOfLine)-                     <*>          (parseOS  <* endOfLine)-                     <*> optional (parseOG  <* endOfLine)-                     <*>          (parseOC  <* endOfLine)-                     <*> optional (parseOX  <* endOfLine)-                     <*> many'    (parseOH  <* endOfLine)-                     <*> many'    (parseRef <* endOfLine)-                     <*> many'    (parseCC  <* endOfLine)-                     <*> many'    (parseDR  <* endOfLine)-                     <*>          (parsePE  <* endOfLine)-                     <*>          (parseKW  <* endOfLine)-                     <*> many'    (parseFT  <* endOfLine)-                     <*>          (parseSQ  <* endOfLine)-                     <*           parseEnd+parseRecord = Record <$>           (parseID  <* endOfLine)+                     <*>           (parseAC  <* endOfLine)+                     <*>           (parseDT  <* endOfLine)+                     <*>           (parseDE  <* endOfLine)+                     <*> option [] (parseGN  <* endOfLine)+                     <*>           (parseOS  <* endOfLine)+                     <*> optional  (parseOG  <* endOfLine)+                     <*>           (parseOC  <* endOfLine)+                     <*>           (parseOX  <* endOfLine)+                     <*> many'     (parseOH  <* endOfLine)+                     <*> many'     (parseRef <* endOfLine)+                     <*> many'     (parseCC  <* endOfLine)+                     <*> many'     (parseDR  <* endOfLine)+                     <*>           (parsePE  <* endOfLine)+                     <*> optional  (parseKW  <* endOfLine)+                     <*> many'     (parseFT  <* endOfLine)+                     <*>           (parseSQ  <* endOfLine)+                     <*            parseEnd  -- = Helper parsers  -- |Transforms any parser to a parser of maybe value.+-- -- >>> parseOnly (optional digit) "1" -- Right (Just 1) --@@ -411,7 +413,7 @@     comm <- (:) <$> parseTillEnd                 <*> many' (do endOfLine                               string start-                              count (skip - 1) space -- leave one space to separate words+                              count (skip - 1) (char ' ') -- leave one space to separate words                               parseTillEnd)     pure $ hyphenConcat comm @@ -429,6 +431,12 @@ hyphenConcat :: [String] -> String hyphenConcat []       = [] hyphenConcat [x]      = x-hyphenConcat (x:y:ys) = if last x == '-'-                          then x ++ tail y ++ hyphenConcat ys-                          else x ++ y ++ hyphenConcat ys+hyphenConcat (x:y:ys) = x ++ hyphenConcat (sy:ys)+  where+    sy :: String+    sy | last x == '-'                  = tail y+       | isAA (last x) && isAA (y !! 1) = tail y+       | otherwise                      = y+    +    isAA :: Char -> Bool+    isAA = inClass "ACDEFGHIKLMNPQRSTVWY"

@@ -246,13 +246,13 @@   , os   :: OS   , og   :: Maybe OG   , oc   :: OC-  , ox   :: Maybe OX+  , ox   :: OX   , oh   :: [OH]   , refs :: [Reference]   , cc   :: [CC]   , dr   :: [DR]   , pe   :: PE-  , kw   :: KW+  , kw   :: Maybe KW   , ft   :: [FT]   , sq   :: SQ   } deriving (Show, Eq, Ord)

@@ -941,6 +941,6 @@       it "parses PD1 example" $ do         let record = Record idAns acAns dtAns deAns                             gnAns osAns Nothing ocAns-                            (Just oxAns) [] refAns ccAns-                            drAns peAns kwAns ftAns sqAns+                            oxAns [] refAns ccAns+                            drAns peAns (Just kwAns) ftAns sqAns         parseOnly parseRecord pd1Str `shouldBe` Right record

@@ -2,10 +2,10 @@ -- -- see: https://github.com/sol/hpack ----- hash: 35141853a683c97f0604c324c743203061f6bba440e50259a2f29dcc8d8825cc+-- hash: 46801dc834178bde36de5bfcd64e4b397b76da7ac4dbe6f22b7275f5a1661110  name:           uniprot-kb-version:        0.1.0.0+version:        0.1.0.1 synopsis:       UniProt-KB format parser description:    Specification implementation of https://web.expasy.org/docs/userman.html category:       Bio