ClustalParser 1.0.3 → 1.1.0

raw patch · 7 files changed

+77/−31 lines, 7 filesdep +either-unwrapdep +hspecdep +vectordep ~basedep ~parsecPVP ok

version bump matches the API change (PVP)

Dependencies added: either-unwrap, hspec, vector

Dependency ranges changed: base, parsec

API changes (from Hackage documentation)

Files

• ClustalParser.cabal +12/−7
• ClustalParserTest.hs +5/−2
• README.md +7/−4
• changelog +3/−0
• src/Bio/ClustalData.hs +36/−2
• src/Bio/ClustalParser.hs +12/−16
• test-suite/Spec.hs +2/−0

@@ -5,9 +5,9 @@ -- PVP summary:      +-+------- breaking API changes --                   | | +----- non-breaking API additions --                   | | | +--- code changes with no API change-version:             1.0.3+version:             1.1.0 synopsis:            Libary for parsing Clustal tools output-description:         Currently contains parsers and datatypes for: clustalw2, clustalo+description:         Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna                      .                      For more information on clustal Tools refer to <http://www.clustal.org/>                      .@@ -33,8 +33,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/ClustalParser/tree/1.0.3-  tag:      1.0.3+  location: https://github.com/eggzilla/ClustalParser/tree/1.1.0+  tag:      1.1.0  library   -- Modules exported by the library.@@ -42,7 +42,7 @@   other-modules:     Bio.ClustalData    -- Other library packages from which modules are imported.-  build-depends:       base >=4.5 && <5, parsec+  build-depends:       base >=4.5 && <5, parsec>=3.1.9, vector   -- compiler options   ghc-options:         -Wall -O2 -fno-warn-unused-do-bind   -- Directories containing source files.@@ -50,7 +50,12 @@    executable ClustalParserTest   main-is:          ClustalParserTest.hs-  build-depends:    base >= 4 && <= 5, cmdargs, ClustalParser+  build-depends:    base >= 4 && <= 5, cmdargs, ClustalParser, either-unwrap   -- compiler options     ghc-options:         -Wall -O2-  ++test-suite hspec+    build-depends:    base, parsec, ClustalParser, hspec >= 1.8+    hs-source-dirs:   test-suite+    main-is:          Spec.hs+    type:             exitcode-stdio-1.0  

@@ -2,12 +2,15 @@      import System.Environment (getArgs) import Bio.ClustalParser+import Data.Either.Unwrap  main :: IO () main = do   args <- getArgs   let input_file = (head args)                                        -- read Clustal outputfile-  parsedinput <- readStructuralClustalAlignment input_file-  print parsedinput+  parsedinput <- readClustalAlignment input_file+  --parsedinput <- readStructuralClustalAlignment input_file+  --print (entrySequenceIdentifier (head (structuralAlignmentEntries(fromRight parsedinput))))+  print (fromRight parsedinput)  

@@ -1,12 +1,15 @@-ClustalParser   [![Build Status](https://travis-ci.org/eggzilla/ClustalParser.svg)](https://travis-ci.org/eggzilla/ClustalParser)+ClustalParser [![Hackage](https://img.shields.io/hackage/v/ClustalParser.svg)](https://hackage.haskell.org/package/ClustalParser) [![Build Status](https://travis-ci.org/eggzilla/ClustalParser.svg)](https://travis-ci.org/eggzilla/ClustalParser) ============= -Currently contains parsers and datatypes for: clustalw2, clustalo+Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna -Clustal tools are multipe sequence aligenment tools for biological sequences +Clustal tools are multiple sequence alignment tools for biological sequences  like DNA, RNA and Protein. For more information on clustal Tools refer to <http://www.clustal.org/>. +Mlocarna is a multiple sequence alignment tool for RNA sequences with+secondary structure output. +For more information on molocarna refer to <http://www.clustal.org/>.  4 types of output are parsed @@ -14,7 +17,7 @@   * Parsing with readClustalAlignment from filepath (Bio.ClustalParser)   * Parsing with parseClustalAlignment from String (Bio.ClustalParser)   -- Alignment file with secondary structure (.aln): + - Alignment file with secondary structure (.aln):    * Parsing with readStructuralClustalAlignment from filepath (Bio.ClustalParser)   * Parsing with parsStructuralClustalAlignment from String (Bio.ClustalParser) 

@@ -1,4 +1,7 @@ -*-change-log-*-+1.1.0 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 1. July 2015+        * Added Hspec test-suite for Parsing functions+	* Added Show instances for ClustalAlignment and StructuralClustalAlignment 1.0.3 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 19. April 2015 	* Added Y (pyrimidine) and R (purine) to sequence characters 1.0.2 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 19. March 2015

@@ -2,6 +2,7 @@ --   For more information on Clustal tools consult: <http://www.clustal.org/>  module Bio.ClustalData where+import qualified Data.Vector as V      -- | Data type for clustal summary, containing information about the alignment process, usually printed to STDOUT data ClustalSummary = ClustalSummary@@ -48,8 +49,32 @@     alignmentEntries :: [ClustalAlignmentEntry],     conservationTrack :: String   }-  deriving (Show, Eq)+  deriving (Eq) +instance Show ClustalAlignment where+  show (ClustalAlignment _alignmentEntries _conservationTrack ) +    | not (null _alignmentEntries) = header ++ alignmentString+    | otherwise = header+    where header = "CLUSTAL W (1.8) multiple sequence alignment\n\n\n" +          longestSequenceIdLength =  (maximum (map length (map entrySequenceIdentifier _alignmentEntries))) + 1+          totalSequenceLength = length (entryAlignedSequence (head _alignmentEntries))+          alignmentString = showAlignment totalSequenceLength longestSequenceIdLength 0 _alignmentEntries _conservationTrack++showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> String -> String+showAlignment totalSequenceLength longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack+  | totalSequenceLength == 0 = [] +  | currentWindowPosition <= totalSequenceLength = showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack ++ (showAlignment totalSequenceLength longestSequenceIdLength (currentWindowPosition + 60) _alignmentEntries _conservationTrack)+  | otherwise = "" ++showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> String -> String+showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack = blockString+  where blockString = entries ++ extraTrack ++ "\n"+        entries = concatMap (showAlignmentLine longestSequenceIdLength currentWindowPosition) _alignmentEntries+        extraTrack = concat (replicate longestSequenceIdLength " ") ++ V.toList (V.slice currentWindowPosition 60  (V.fromList _conservationTrack)) ++ "\n"++showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String+showAlignmentLine longestSequenceIdLength currentWindowPosition _alignmentEntry = (entrySequenceIdentifier _alignmentEntry) ++ concat (replicate (longestSequenceIdLength - length (entrySequenceIdentifier _alignmentEntry)) " ") ++ V.toList (V.slice currentWindowPosition 60  (V.fromList (entryAlignedSequence _alignmentEntry))) ++ "\n"+ data ClustalAlignmentEntry = ClustalAlignmentEntry   {     entrySequenceIdentifier :: String,@@ -79,7 +104,16 @@     secondaryStructureTrack :: String,     energy :: Double   }-  deriving (Show, Eq)+  deriving (Eq)++instance Show StructuralClustalAlignment where+  show (StructuralClustalAlignment _alignmentEntries _secondaryStructureTrack _energy) +    | not (null _alignmentEntries) = header ++ alignmentString+    | otherwise = header+    where header = "CLUSTAL W \n\n" +          longestSequenceIdLength =  (maximum (map length (map entrySequenceIdentifier _alignmentEntries))) + 1+          totalSequenceLength = length (entryAlignedSequence (head _alignmentEntries))+          alignmentString = showAlignment totalSequenceLength longestSequenceIdLength 0 _alignmentEntries _secondaryStructureTrack  data StructuralClustalAlignmentSlice = StructuralClustalAlignmentSlice   {

@@ -118,14 +118,14 @@   newline   newline   newline-  alignmentSlices <- many1 genParserClustalAlignmentSlice+  alignmentSlices <- many1 (try genParserClustalAlignmentSlice)   eof     return (mergealignmentSlices alignmentSlices)  mergealignmentSlices :: [ClustalAlignmentSlice] -> ClustalAlignment mergealignmentSlices slices = alignment   where entrySlicesList = map entrySlices slices -- list of lists of entry slices-        sequenceIdentifiers = map entrySequenceSliceIdentifier (head entrySlicesList)+        sequenceIdentifiers = nub (map entrySequenceSliceIdentifier (head entrySlicesList))         alignmentEntriesListBySlice =  map (map entryAlignedSliceSequence) entrySlicesList           transposedAlignmentEntriesListbySlice = transpose alignmentEntriesListBySlice         mergedAlignmentSequenceEntries = map concat transposedAlignmentEntriesListbySlice@@ -152,7 +152,7 @@ genParserClustalEntrySlice = do   sliceIdentifier <- many1 (noneOf " ")   spacer <- many1 (char ' ')-  sliceSequence <- many1 (oneOf "NYRUAGCT-")+  sliceSequence <- many1 (oneOf "SNYRUAGCT-")   newline   return $ ClustalAlignmentEntrySlice sliceIdentifier sliceSequence (length spacer) @@ -189,29 +189,25 @@  genParseMlocarnaHeader :: GenParser Char st String genParseMlocarnaHeader = do-  string "mLo"-  many1 (noneOf "\n")+  string "mLocARNA"+  many1 (choice [alphaNum,oneOf "-: ()."])   newline   string "Copyright"-  many1 (noneOf "\n")+  many1 (choice [alphaNum,char ' '])   newline   newline  -  many1 genParseAlignmentProcessStep+  string "Compute pair probs ..."   newline+  string "Perform progressive alignment ..."   newline-  return ""--genParseAlignmentProcessStep :: GenParser Char st String-genParseAlignmentProcessStep = do-  many1 (noneOf ".\n")-  choice [try (string ("... ")), try (string ("..."))]   newline+  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)+        sequenceIdentifiers = (map structuralEntrySequenceSliceIdentifier (head entrySlicesList))         alignmentEntriesListBySlice =  map (map structuralEntryAlignedSliceSequence) entrySlicesList           transposedAlignmentEntriesListbySlice = transpose alignmentEntriesListBySlice         mergedAlignmentSequenceEntries = map concat transposedAlignmentEntriesListbySlice@@ -231,7 +227,7 @@ genParserStructuralClustalEntrySlice = do   sliceIdentifier <- many1 (noneOf " ")   many1 (char ' ')-  sliceSequence <- many1 (oneOf "NYRUAGCT-")+  sliceSequence <- many1 (oneOf "SNYRUAGCT-")   newline   return $ StructuralClustalAlignmentEntrySlice (filter (/='\n') sliceIdentifier) sliceSequence @@ -247,7 +243,7 @@  -- | 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"+parseStructuralClustalAlignment = parse genParserStructuralClustalAlignment "genParserStructuralClustalAlignment"  -- | Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from filehandle (as produced by mlocarna)                   readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment)   

@@ -0,0 +1,2 @@+-- test-suite/Spec.hs+{-# OPTIONS_GHC -F -pgmF hspec-discover #-}