ClustalParser 1.0.0 → 1.0.1

raw patch · 4 files changed

+130/−30 lines, 4 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• ClustalParser.cabal +8/−4
• ClustalParserTest.hs +2/−4
• src/Bio/ClustalData.hs +16/−7
• src/Bio/ClustalParser.hs +104/−15

@@ -5,7 +5,7 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.0.0+version:             1.0.1 synopsis:            Libary for parsing Clustal tools output description:         Currently contains parsers and datatypes for: clustalw2, clustalo                      .@@ -30,8 +30,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/ClustalParser/tree/1.0.0-  tag:      1.0.0+  location: https://github.com/eggzilla/ClustalParser/tree/1.0.1+  tag:      1.0.1  library   -- Modules exported by the library.@@ -40,10 +40,14 @@    -- Other library packages from which modules are imported.   build-depends:       base >=4.5 && <5, parsec-  +  -- compiler options+  ghc-options:         -Wall -O2 -fno-warn-unused-do-bind   -- Directories containing source files.   hs-source-dirs:      src    executable ClustalParserTest   main-is:          ClustalParserTest.hs   build-depends:    base >= 4 && <= 5, cmdargs, ClustalParser+  -- compiler options  +  ghc-options:         -Wall -O2+  

@@ -1,11 +1,9 @@ module Main where      import System.Environment (getArgs)-import System.IO-import System.Environment import Bio.ClustalParser-import Data.Either-    ++main :: IO () main = do   args <- getArgs   let input_file = (head args)                                     

@@ -42,7 +42,6 @@   }   deriving (Show, Eq) - -- | Data structure for Clustal alignment format data ClustalAlignment = ClustalAlignment   { @@ -73,16 +72,26 @@   }   deriving (Show, Eq) -data ClustalGuideTree = ClustalGuideTree+-- | Data structure for structural Clustal alignment format+data StructuralClustalAlignment = StructuralClustalAlignment   { -    guideTreeEntries :: [ClustalGuideTreeEntry]+    structuralAlignmentEntries :: [ClustalAlignmentEntry],+    secondaryStructureTrack :: String,+    energy :: Double   }   deriving (Show, Eq) -data ClustalGuideTreeEntry = ClustalGuideTreeEntry-  { -    entryDesignation :: String,-    entryDistance :: Double+data StructuralClustalAlignmentSlice = StructuralClustalAlignmentSlice+  {+    structuralEntrySlices :: [StructuralClustalAlignmentEntrySlice]   }   deriving (Show, Eq)++data StructuralClustalAlignmentEntrySlice = StructuralClustalAlignmentEntrySlice+  {+    structuralEntrySequenceSliceIdentifier :: String,+    structuralEntryAlignedSliceSequence :: String+  }+  deriving (Show, Eq)+ 

@@ -1,17 +1,17 @@ -- | Parse Clustal output-+--   For more information on Clustal tools consult: <http://www.clustal.org/> module Bio.ClustalParser (                        parseClustalAlignment,                        readClustalAlignment,+                       parseStructuralClustalAlignment,+                       readStructuralClustalAlignment,                        parseClustalSummary,                        readClustalSummary,                        module Bio.ClustalData                       ) where  import Bio.ClustalData-import Text.ParserCombinators.Parsec-import Text.ParserCombinators.Parsec.Token-import Text.ParserCombinators.Parsec.Language (emptyDef)    +import Text.ParserCombinators.Parsec     import Control.Monad import Data.List @@ -35,7 +35,7 @@   newline   newline   string "Sequence format is "-  sequenceFormat <- many1 (noneOf "\n")+  sequenceFormat' <- many1 (noneOf "\n")   newline   sequenceParametersList <- many1 (try genParserSequenceParameters)   string "Start of Pairwise alignments" @@ -45,7 +45,7 @@   newline   pairwiseAlignmentSummaryList <- many1 genParserPairwiseAlignmentSummary   string "Guide tree file created:   ["-  guideTreeFileName <- many1 (noneOf "]")+  guideTreeFileName' <- many1 (noneOf "]")   char ']'   newline   newline@@ -60,16 +60,16 @@   newline   groupSummaryList <- many1 genParserGroupSummary   string "Alignment Score "-  alignmentScore <- many1 digit+  alignmentScore' <- many1 digit   newline   newline   string "CLUSTAL-Alignment file created  ["-  alignmentFileName <- many1 (noneOf "]")+  alignmentFileName' <- many1 (noneOf "]")   char ']'   newline   newline   eof  -  return $ ClustalSummary version sequenceFormat sequenceParametersList pairwiseAlignmentSummaryList guideTreeFileName (readInt numberOfGroups) groupSummaryList (readInt alignmentScore) alignmentFileName+  return $ ClustalSummary version sequenceFormat' sequenceParametersList pairwiseAlignmentSummaryList guideTreeFileName' (readInt numberOfGroups) groupSummaryList (readInt alignmentScore') alignmentFileName'  genParserGroupSummary :: GenParser Char st GroupSummary genParserGroupSummary = do@@ -82,9 +82,9 @@   sequenceNumber <- optionMaybe (many1 digit)   optional (many1 space)   string "Score:" <|>  string "Delayed"-  groupScore <- optionMaybe (many1 digit) +  groupScore' <- optionMaybe (many1 digit)    newline-  return $ GroupSummary (readInt groupIndex) (liftM readInt sequenceNumber) (liftM readInt groupScore)+  return $ GroupSummary (readInt groupIndex) (liftM readInt sequenceNumber) (liftM readInt groupScore')  genParserPairwiseAlignmentSummary :: GenParser Char st PairwiseAlignmentSummary genParserPairwiseAlignmentSummary = do@@ -139,14 +139,14 @@  genParserClustalAlignmentSlice :: GenParser Char st ClustalAlignmentSlice genParserClustalAlignmentSlice = do-  entrySlices <- many1 genParserClustalEntrySlice+  entrySlices' <- many1 genParserClustalEntrySlice   --extract length of identifier and spacer to determine offset of conservation track-  let offsetLenght = length (entrySequenceSliceIdentifier (head entrySlices)) + spacerLength (head entrySlices)+  let offsetLenght = length (entrySequenceSliceIdentifier (head entrySlices')) + spacerLength (head entrySlices')   spacerAndConservationTrackSlice <- many1 (noneOf "\n")-  let conservationTrackSlice = drop offsetLenght spacerAndConservationTrackSlice+  let conservationTrackSlice' = drop offsetLenght spacerAndConservationTrackSlice   newline   optional newline-  return $ ClustalAlignmentSlice entrySlices conservationTrackSlice+  return $ ClustalAlignmentSlice entrySlices' conservationTrackSlice'  genParserClustalEntrySlice :: GenParser Char st ClustalAlignmentEntrySlice genParserClustalEntrySlice = do@@ -156,6 +156,87 @@   newline   return $ ClustalAlignmentEntrySlice sliceIdentifier sliceSequence (length spacer) +--Structural Clustal Parser functions++-- | Parse the input as ClustalAlignment datatype as used in mlocarna+genParserStructuralClustalAlignment :: GenParser Char st StructuralClustalAlignment+genParserStructuralClustalAlignment = do+  genParseMlocarnaHeader+  alignmentSlices <- many1 (try genParserStructuralClustalAlignmentSlice)+  secondaryStructure <- genSecondaryStructure  +  energy' <- genParseEnergy+  eof  +  return (mergeStructuralAlignmentSlices alignmentSlices secondaryStructure energy')++genSecondaryStructure :: GenParser Char st String+genSecondaryStructure = do+  string "alifold"+  many1 space+  secondaryStructure <- many1 (oneOf ".()")+  space+  return secondaryStructure++genParseEnergy :: GenParser Char st Double+genParseEnergy = do+  string "("+  many space +  energy' <- many1 (noneOf " ")+  optional space+  char ('=')+  many1 (noneOf "\n")+  newline  +  return (readDouble energy')++genParseMlocarnaHeader :: GenParser Char st String+genParseMlocarnaHeader = do+  string "mLo"+  many1 (noneOf "\n")+  newline+  string "Copyright"+  many1 (noneOf "\n")+  newline+  newline  +  many1 genParseAlignmentProcessStep+  newline+  newline+  return ""++genParseAlignmentProcessStep :: GenParser Char st String+genParseAlignmentProcessStep = do+  many1 (noneOf ".\n")+  choice [try (string ("... ")), try (string ("..."))]+  newline+  return ""++mergeStructuralAlignmentSlices :: [StructuralClustalAlignmentSlice] -> String -> Double -> StructuralClustalAlignment+mergeStructuralAlignmentSlices slices secondaryStructure energy' = alignment+  where entrySlicesList = map structuralEntrySlices slices -- list of lists of entry slices+        sequenceIdentifiers = map structuralEntrySequenceSliceIdentifier (head entrySlicesList)+        alignmentEntriesListBySlice =  map (map structuralEntryAlignedSliceSequence) entrySlicesList  +        transposedAlignmentEntriesListbySlice = transpose alignmentEntriesListBySlice+        mergedAlignmentSequenceEntries = map concat transposedAlignmentEntriesListbySlice+        mergedAlignmentEntries = map constructStructuralAlignmentEntries (zip sequenceIdentifiers mergedAlignmentSequenceEntries)+        alignment = StructuralClustalAlignment mergedAlignmentEntries secondaryStructure energy' ++constructStructuralAlignmentEntries :: (String, String) -> ClustalAlignmentEntry+constructStructuralAlignmentEntries (entryIdentifier,entrySequence) = ClustalAlignmentEntry entryIdentifier entrySequence++genParserStructuralClustalAlignmentSlice :: GenParser Char st StructuralClustalAlignmentSlice+genParserStructuralClustalAlignmentSlice = do+  entrySlices' <- many1 (try genParserStructuralClustalEntrySlice)+  optional newline+  return $ StructuralClustalAlignmentSlice entrySlices'++genParserStructuralClustalEntrySlice :: GenParser Char st StructuralClustalAlignmentEntrySlice+genParserStructuralClustalEntrySlice = do+  sliceIdentifier <- many1 (noneOf " ")+  many1 (char ' ')+  sliceSequence <- many1 (oneOf "UAGCT-")+  newline+  return $ StructuralClustalAlignmentEntrySlice sliceIdentifier sliceSequence++-- exported functions+ -- | Parse Clustal alignment (.aln) from String parseClustalAlignment :: String -> Either ParseError ClustalAlignment  parseClustalAlignment = parse genParserClustalAlignment "genParserClustalAlignment"@@ -163,6 +244,14 @@ -- | Parse Clustal alignment (.aln) from filehandle                   readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment)    readClustalAlignment = parseFromFile genParserClustalAlignment++-- | Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from String (as produced by mlocarna)+parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment +parseStructuralClustalAlignment = parse genParserStructuralClustalAlignment "genParserClustalAlignment"++-- | Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from filehandle (as produced by mlocarna)                  +readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment)   +readStructuralClustalAlignment = parseFromFile genParserStructuralClustalAlignment  -- |  Parse Clustal summary (printed to STDOUT) from String parseClustalSummary :: String -> Either ParseError ClustalSummary