BioHMM 1.0.0 → 1.0.1

raw patch · 4 files changed

+110/−4 lines, 4 files

Files

• BioHMM.cabal +4/−3
• README.md +1/−1
• changelog +2/−0
• src/Bio/HMMCompareResult.hs +103/−0

@@ -1,5 +1,5 @@ name:                BioHMM-version:             1.0.0+version:             1.0.1 synopsis:            Libary containing parsing and visualisation functions and datastructures for Hidden Markov Models in HMMER3 format.  -- description:          license:             GPL-3@@ -20,14 +20,15 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/HMM/tree/1.0.0-  tag:      1.0.0+  location: https://github.com/eggzilla/HMM/tree/1.0.1+  tag:      1.0.1  library   -- Modules exported by the library.   exposed-modules:   Bio.HMMData                      Bio.HMMParser                      Bio.HMMDraw+                     Bio.HMMCompareResult    -- compiler-options:   ghc-options:         -Wall -O2 -fno-warn-unused-do-bind

@@ -1,4 +1,4 @@-HMM+BioHMM [![Hackage](https://img.shields.io/hackage/v/BioHMM.svg)](https://hackage.haskell.org/package/BioHMM) [![Build Status](https://travis-ci.org/eggzilla/BioHMM.svg?branch=master)](https://travis-ci.org/eggzilla/BioHMM) ====  Libary containing parsing and visualisation functions, as well as datastructures for Hidden Markov Models in HMMER3 format.

@@ -1,3 +1,5 @@ -*-change-log-*-+1.0.1 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 22. December 2016+        * Bugfix - added Bio.HMMCompare to exported modules 1.0.0 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 22. December 2016         * Initial release

@@ -0,0 +1,103 @@+-- | Parse HMMCompare output++module Bio.HMMCompareResult+    (+     HMMCompareResult,+     parseHMMCompareResult,+     readHMMCompareResult,+     model1Name,+     model2Name,+     linkscore1, +     linkscore2,+     linksequence,+     model1matchednodes,+     model2matchednodes,+     getHMMCompareResults,+     getModelsNames,+     getModelNames+    ) where++import Text.ParserCombinators.Parsec     +import Control.Monad++-- | Datastructure for result strings of comparisons between covariance models by HMMCompare+data HMMCompareResult = HMMCompareResult           +  { model1Name :: String,+    model2Name :: String,+    linkscore1 :: Double,+    linkscore2 :: Double,+    linksequence  :: String,+    model1matchednodes :: [Int],+    model2matchednodes :: [Int]+  } deriving (Show)++-- | parse HMMCompareResult model from input string+parseHMMCompareResult :: [Char] -> Either ParseError [HMMCompareResult]+parseHMMCompareResult input = parse genParseHMMCompareResults "HMMCompareResult" input++-- | parse HMMCompareResult from input filePath                      +readHMMCompareResult :: String -> IO (Either ParseError [HMMCompareResult])                  +readHMMCompareResult filePath = do +  parsedFile <- parseFromFile genParseHMMCompareResults filePath+  return parsedFile++-- | Parse the input as HMMCompareResult datatype+genParseHMMCompareResults :: GenParser Char st [HMMCompareResult]+genParseHMMCompareResults = do+  hmmcs  <- many1 (try genParseHMMCompareResult)+  eof+  return hmmcs++readDouble :: String -> Double+readDouble = read              ++readInt :: String -> Int+readInt = read++-- | Parse a HMMCompare result string+genParseHMMCompareResult :: GenParser Char st HMMCompareResult+genParseHMMCompareResult = do+    name1 <-  many1 (noneOf " ")+    _ <- many1 space+    name2 <-  many1 (noneOf " ")+    _ <- many1 space+    score1 <- many1 (noneOf " ")+    _ <- many1 space+    score2 <- many1 (noneOf " ")+    _ <- many1 space+    linkseq <- many1 (oneOf "AGTCUagtcu")+    _ <- many1 space+    _ <- char '['+    nodes1 <- many1 parseMatchedNodes+    _ <- char ']'+    _ <- many1 space+    _ <- char '['+    nodes2 <- many1 parseMatchedNodes+    _ <- char ']'+    newline+    return $ HMMCompareResult name1 name2 (readDouble score1) (readDouble score2) linkseq nodes1 nodes2++-- | Parse indices of matched nodes between models as integers+parseMatchedNodes :: GenParser Char st Int +parseMatchedNodes = do+    nodeNumber <- many1 digit+    optional (char ',')+    return $ (readInt nodeNumber)++-- | Parser for HMMCompare result strings+getHMMCompareResults :: FilePath -> IO [Either ParseError HMMCompareResult]    +getHMMCompareResults filePath = let+        fp = filePath+        doParseLine' = parse genParseHMMCompareResult "genParseHMMCompareResults"+        --doParseLine l = case (doParseLine' l) of+        --    Right x -> x+        --    Left _  -> error "Failed to parse line"+    in do+        fileContent <- liftM lines $ readFile fp+        return $ map doParseLine' fileContent++getModelsNames :: [HMMCompareResult] -> [String]+getModelsNames models = concat (map getModelNames models)++getModelNames :: HMMCompareResult -> [String]+getModelNames model = [model1Name model,model2Name model]