diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,705 @@ +Copyright Gregory W. Schwartz (c) 2015 + +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright + notice, this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above + copyright notice, this list of conditions and the following + disclaimer in the documentation and/or other materials provided + with the distribution. + + * Neither the name of Gregory W. 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If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + {project} Copyright (C) {year} {fullname} + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/Setup.hs b/Setup.hs new file mode 100644 --- /dev/null +++ b/Setup.hs @@ -0,0 +1,2 @@ +import Distribution.Simple +main = defaultMain diff --git a/app/Main.hs b/app/Main.hs new file mode 100644 --- /dev/null +++ b/app/Main.hs @@ -0,0 +1,173 @@ +{- Main +by Gregory Schwartz + +-- | Computes a BLOSUM, but takes into account alternate amino acids +-} +module Main where + +-- Standard +import Data.Maybe +import qualified Data.Map.Strict as Map +import qualified Data.Sequence as Seq +import qualified System.IO as IO +import qualified Data.List.Split as Split +import Debug.Trace + +-- Cabal +import qualified Data.Text as T +import qualified Data.Text.IO as T +import Data.Fasta.Text +import Pipes +import qualified Pipes.Prelude as P +import qualified Pipes.Text.IO as PT +import Options.Applicative + +-- Local +import Types +import Utility +import Cluster +import Matrix +import Print + +-- Command line arguments +data Options = Options { input :: Maybe String + , identity :: Double + , blockField :: Maybe Int + , csv :: Maybe String + , badChars :: Maybe String + , allFlag :: Bool + , output :: Maybe String + } + +-- Command line options +options :: Parser Options +options = Options + <$> optional ( strOption + ( long "input" + <> short 'i' + <> metavar "FILE" + <> help "The input fasta file with blocks labeled in a field.\ + \ If empty, then assumed to use stdin to send the many, many\ + \ filenames, where each file is a block." + ) + ) + <*> option auto + ( long "identity" + <> short 'd' + <> metavar "[100] | PERCENT" + <> value 100 + <> help "The percent identity of two sequences for clustering.\ + \ BLOSUM's most famous identity is 62" ) + <*> optional ( option auto + ( long "field" + <> short 'f' + <> metavar "FIELD" + <> help "The field in the fasta headers (1 indexed) which says\ + \ the block it belongs to. Assumed to already be next to\ + \ each other, so the block members should not be scattered" + ) + ) + <*> optional ( strOption + ( long "csv" + <> short 'c' + <> metavar "STRING" + <> help "Print the output as a 2D csv using this ordering" ) + ) + <*> optional ( strOption + ( long "remove-characters" + <> short 'b' + <> metavar "STRING" + <> help "Whether to remove this character from individual sequences\ + \ that have at least one of these characters" + ) + ) + <*> switch + ( long "all-remove-characters" + <> short 'B' + <> help "Whether to remove all positions that have at least one of the\ + \ characters from remove-character" + ) + <*> optional ( strOption + ( long "output" + <> short 'o' + <> metavar "FILE" + <> help "The output file containing the matrix" + ) + ) + +-- | Get a frequency map from a single file +getFrequencyMapSingleFile :: Options -> FilePath -> IO FrequencyMap +getFrequencyMapSingleFile opts file = do + h <- IO.openFile file IO.ReadMode + fastaList <- runEffect $ P.toListM $ pipesFasta . PT.fromHandle $ h + + let clusters = getClusterIdentity (Identity $ identity opts) + clusterMaps = Map.elems + . Map.map getClusterFrequencyMap + . unClusterMap + blockMaps = fmap ( getBlockMap + (allFlag opts) + ((fmap . fmap) AA $ badChars opts) + ) + . fmap clusterMaps + . fmap clusters + . fmap Seq.fromList + . groupBlocks (fmap Field $ blockField opts) + $ fastaList + frequencyMap = joinBlockMaps blockMaps + + return frequencyMap + +-- | Get a block from a filepath +getBlock :: Options -> FilePath -> IO BlockMap +getBlock opts file = do + h <- IO.openFile file IO.ReadMode + fastaList <- runEffect $ P.toListM $ pipesFasta . PT.fromHandle $ h + + let clusters = getClusterIdentity (Identity $ identity opts) + clusterMap = Map.elems + . Map.map getClusterFrequencyMap + . unClusterMap + blockMap = getBlockMap + (allFlag opts) + ((fmap . fmap) AA $ badChars opts) + . clusterMap + . clusters + . Seq.fromList + $ fastaList + + return blockMap + +blosum :: Options -> IO () +blosum opts = do + + frequencyMap <- + case input opts of + Nothing -> fmap FrequencyMap + . P.fold (<>) (AAMap Map.empty) id + $ P.stdinLn + >-> P.mapM (fmap unBlockMap . getBlock opts) + (Just x) -> getFrequencyMapSingleFile opts x + + let blosumMatrix = getBlosum frequencyMap + result = case csv opts of + (Just x) -> printBlosumCSV + (map AA x) + blosumMatrix + Nothing -> printBlosum blosumMatrix + + + + -- Save results + case output opts of + Nothing -> T.putStrLn result + (Just x) -> T.writeFile x result + +main :: IO () +main = execParser opts >>= blosum + where + opts = info (helper <*> options) + ( fullDesc + <> progDesc "Computes a BLOSUM, but takes into account\ + \ alternate amino acids" + ) diff --git a/blosum.cabal b/blosum.cabal new file mode 100644 --- /dev/null +++ b/blosum.cabal @@ -0,0 +1,48 @@ +name: blosum +version: 0.1.1.1 +synopsis: BLOSUM generator +description: Please see README.md +homepage: http://github.com/GregorySchwartz/blosum#readme +license: GPL-2 +license-file: LICENSE +author: Gregory W. Schwartz +maintainer: gregory.schwartz@drexel.edu +copyright: Copyright 2016 Gregory W. Schwartz +category: Bioinformatics +build-type: Simple +-- extra-source-files: +cabal-version: >=1.10 + +library + hs-source-dirs: src + exposed-modules: Types + , Utility + , Cluster + , Matrix + , Print + build-depends: base >= 4.7 && < 5 + , containers + , text + , text-show + , fasta + , lens + default-language: Haskell2010 + +executable blosum + hs-source-dirs: app + main-is: Main.hs + ghc-options: -threaded -rtsopts -with-rtsopts=-N -O2 + build-depends: base + , blosum + , containers + , fasta + , text + , split + , pipes + , pipes-text + , optparse-applicative + default-language: Haskell2010 + +source-repository head + type: git + location: https://github.com/GregorySchwartz/blosum diff --git a/src/Cluster.hs b/src/Cluster.hs new file mode 100644 --- /dev/null +++ b/src/Cluster.hs @@ -0,0 +1,80 @@ +{- Cluster +by Gregory Schwartz + +-- | Collects the functions pertaining to the clustering of sequences by hamming +distance identity +-} + +{-# LANGUAGE BangPatterns #-} +{-# LANGUAGE ViewPatterns #-} + +module Cluster + ( getClusterIdentity + , groupBy' + ) where + +-- Standard +import qualified Data.Map.Strict as Map +import qualified Data.Sequence as Seq +import qualified Data.Foldable as F + +-- Cabal +import qualified Data.Text as T +import Data.Fasta.Text + +-- Local +import Types + +-- | Like hamming, but similarity rather than distance +negHamming :: T.Text -> T.Text -> Double +negHamming x = sum . map (\(x, y) -> if x == y then 1 else 0) . T.zip x + +-- | Takes in an identity and fasta sequences and returns the sequences +-- grouped together by hamming distance identity +getClusterIdentity :: Identity + -> Seq.Seq FastaSequence + -> ClusterMap +getClusterIdentity identity = ClusterMap + . Map.fromList + . zip [1..] + . clusterIdentityGo identity + +-- | Keep comparing clusters until no more fusions (no change in size) make +-- sense +clusterIdentityGo :: Identity + -> Seq.Seq FastaSequence + -> [Seq.Seq FastaSequence] +clusterIdentityGo identity = F.toList + . groupBy' (compareSeqs identity) + +-- | Group together by all pairings rather than adjacent. Altered from +-- lyxia's original to use sequences. +groupBy' :: (a -> a -> Bool) -> Seq.Seq a -> Seq.Seq (Seq.Seq a) +groupBy' _ (Seq.null -> True) = Seq.empty +groupBy' f (Seq.viewl -> x Seq.:< xs) = eqX Seq.<| groupBy' f neqX + where + (!eqX, !neqX) = eqTo f Seq.empty (Seq.singleton x) xs + +-- | Helper to groupBy'. Altered from lyxia's original to use sequences. +eqTo :: (a -> a -> Bool) + -> Seq.Seq a + -> Seq.Seq a + -> Seq.Seq a + -> (Seq.Seq a, Seq.Seq a) +eqTo _ acc (Seq.null -> True) zs = (acc, zs) +eqTo f acc (Seq.viewl -> x Seq.:< xs) zs = + eqTo f (x Seq.<| acc) (eqX Seq.>< xs) neqX + where + (!eqX, !neqX) = Seq.partition (f x) zs + +-- | Either the sequences are similar or not +compareSeqs :: Identity -> FastaSequence -> FastaSequence -> Bool +compareSeqs identity x y = getIdentity x y >= identity + +-- | Get the identity between two sequences +getIdentity :: FastaSequence -> FastaSequence -> Identity +getIdentity xs ys = Identity + . (* 100) + . (/ (fromIntegral . T.length . fastaSeq $ xs)) + . negHamming (fastaSeq xs) + $ (fastaSeq ys) diff --git a/src/Matrix.hs b/src/Matrix.hs new file mode 100644 --- /dev/null +++ b/src/Matrix.hs @@ -0,0 +1,146 @@ +{- Matrix +by Gregory Schwartz + +-- | Collects the functions pertaining to the creation of the BLOSUM +-- matrix +-} + +{-# LANGUAGE BangPatterns #-} +{-# LANGUAGE ViewPatterns #-} + +module Matrix + ( removeChar + , getClusterFrequencyMap + , getBlockMap + , joinBlockMaps + , getBlosum + ) where + +-- Standard +import Data.Maybe +import Data.Tuple +import qualified Data.Map.Strict as Map +import qualified Data.Sequence as Seq +import qualified Data.Foldable as F +import Control.Applicative +import Control.Lens + +-- Cabal +import Data.Fasta.Text + +-- Local +import Types +import Utility + +-- | Zip positions into fasta sequences with a certain size (number of +-- sequences in a cluster) of AA pairs +zipSize :: Frequency -> [AA] -> [(AA, Frequency)] +zipSize x = flip zip [x,x..] + +-- | Zip positions into sequences to get position pairs +zipPosition :: [a] -> [(Position, a)] +zipPosition = zip [1..] + +-- | Get the frequencies of amino acid pairs for each position in a cluster +getClusterFrequencyMap :: Seq.Seq FastaSequence -> ClusterFrequencyMap +getClusterFrequencyMap xs = ClusterFrequencyMap + . Map.map summarize + . Map.fromListWith (Seq.><) + . concat + . F.toList + . fmap positionFrequencies + $ xs + where + summarize = Seq.fromList . zipSize clusterSize . F.toList + positionFrequencies = zipPosition + . map Seq.singleton + . getSeq + clusterSize = Frequency . fromIntegral . Seq.length $ xs + +-- | Filter gaps out of the map. If no gaps are wanted, remove the entire +-- position +removeChar :: Bool -> Maybe [AA] -> AAMap -> AAMap +removeChar _ Nothing = id +removeChar allFlag (Just badChars) = AAMap + . filterBadKey + . Map.map filterBadKey + . removeAll allFlag + . unAAMap + where + removeAll False x = x + removeAll True x = + if or + . map + ( \bad -> Map.member bad x + || (or . Map.elems . Map.map (Map.member bad) $ x) + ) + $ badChars + then Map.empty + else x + filterBadKey = Map.filterWithKey (\k _ -> notElem k badChars) + +collectPairs :: (Ord a, Num b, Fractional b) => Seq.Seq (Seq.Seq (a, b)) + -> Seq.Seq (a, (a, b)) + -> Seq.Seq (a, (a, b)) +collectPairs (Seq.null -> True) !ys = ys +collectPairs (Seq.viewl -> x Seq.:< xs) !ys = + collectPairs xs $ comparisons Seq.>< flippedComparisons Seq.>< ys + where + flippedComparisons = Seq.filter (\a -> fst a /= (fst . snd $ a)) + . fmap (\ (!a, (!b, !c)) -> (b, (a, c))) + $ comparisons + comparisons = F.asum . fmap (pairs x) $ xs + pairs as bs = (\ (!a, !b) (!c, !d) + -> (a, (c, (1 / (b * d)))) + ) + <$> as + <*> bs + +-- Convert a sequence of clusters of sequences of AAs into an amino acid +-- map. We do such a convoluted method in order to make sure we aren't +-- comparing within a cluster, only between clusters. +toAAMap :: Seq.Seq (Seq.Seq (AA, Frequency)) -> AAMap +toAAMap = AAMap + . Map.fromListWith (Map.unionWith (+)) + . F.toList + . fmap (over _2 (uncurry Map.singleton)) + . flip collectPairs Seq.empty + +-- | Get the frequency matrix from a list of frequency maps from clusters. +-- We no longer care about positions after this. +getBlockMap :: Bool -> Maybe [AA] -> [ClusterFrequencyMap] -> BlockMap +getBlockMap allFlag badChars = BlockMap + . mconcat + . Map.elems + . Map.map (removeChar allFlag badChars . toAAMap) + . Map.unionsWith (Seq.><) + . map (Map.map Seq.singleton) -- To separate different clusters + . map unClusterFrequencyMap + +-- | Join together all frequency maps into a single frequency map. +joinBlockMaps :: [BlockMap] -> FrequencyMap +joinBlockMaps = FrequencyMap . mconcat . map unBlockMap + +-- | Get the blosum matrix of each AA entry +getBlosum :: FrequencyMap -> Blosum +getBlosum (FrequencyMap (AAMap frequencyMap)) = + Blosum + . Map.mapWithKey (\k -> Map.mapWithKey (\l _ -> blosum k l)) + $ frequencyMap + where + blosum x y = BlosumVal . round $ 2 * logBase 2 (q x y / e x y) + e x y = if x == y then p x * p y else 2 * p x * p y + p x = q x x + + (sum (map (q x) . filter (/= x) . Map.keys $ frequencyMap) / 2) + q x y = (\(Frequency a) -> a) + $ (lookZero y (lookMap x $ frequencyMap)) + / qDenom + qDenom = (/ 2) + $ (sumMap . Map.map sumMap $ frequencyMap) + + ( sumMap + . Map.mapWithKey + (\k1 -> sumMap . Map.filterWithKey (\k2 _ -> k1 == k2)) + $ frequencyMap + ) + lookZero k = fromMaybe 0 . Map.lookup k + lookMap k = fromMaybe Map.empty . Map.lookup k diff --git a/src/Print.hs b/src/Print.hs new file mode 100644 --- /dev/null +++ b/src/Print.hs @@ -0,0 +1,60 @@ +{- Print +by Gregory Schwartz + +-- | Collects the functions pertaining to the printing of the BLOSUM matrix +-} + +{-# LANGUAGE OverloadedStrings #-} + +module Print + ( printBlosum + , printBlosumCSV + ) where + +-- Standard +import Data.Maybe +import qualified Data.Map.Strict as Map + +-- Cabal +import qualified Data.Text as T +import TextShow + +-- Local +import Types + +-- | Print the BLOSUM matrix as a dataframe +printBlosum :: Blosum -> T.Text +printBlosum = T.append header . T.append "\n" . body . unBlosum + where + header = "source,destination,value" + body = T.unlines + . concatMap Map.elems + . Map.elems + . Map.mapWithKey + ( \(AA x) -> Map.mapWithKey + (\ (AA y) (BlosumVal v) + -> T.intercalate "," [ T.singleton x + , T.singleton y + , showt v + ] + ) + ) + +-- | Print the BLOSUM matrix as a csv matrix according to a certain order +printBlosumCSV :: [AA] -> Blosum -> T.Text +printBlosumCSV order = T.append header . T.append "\n" . body . unBlosum + where + header = T.intercalate "," . ("" :) . map (T.singleton . unAA) $ order + body m = T.unlines + . map ( \x -> T.append (flip T.snoc ',' . T.singleton . unAA $ x) + . fromMaybe "" + . flip Map.lookup (printMap m) + $ x + ) + $ order + printMap :: Map.Map AA (Map.Map AA BlosumVal) -> Map.Map AA T.Text + printMap = Map.map ( \v -> T.intercalate "," + . map (flip lookZero v) + $ order + ) + lookZero k = fromMaybe "" . fmap (showt . unBlosumVal) . Map.lookup k diff --git a/src/Types.hs b/src/Types.hs new file mode 100644 --- /dev/null +++ b/src/Types.hs @@ -0,0 +1,49 @@ +{- Types +by Gregory Schwartz + +-- | Collects the functions pertaining to the types used in the program +-} + +{-# LANGUAGE GeneralizedNewtypeDeriving #-} + +module Types where + +-- Standard +import qualified Data.Map.Strict as Map +import qualified Data.Sequence as Seq + +-- Cabal +import Data.Fasta.Text + +newtype AA = AA { unAA :: Char } deriving (Eq, Ord, Show, Read) +newtype Nuc = Nuc Char deriving (Eq, Ord, Show, Read) +newtype Field = Field Int deriving (Eq) +newtype Frequency = Frequency Double + deriving (Eq, Ord, Num, Enum, Show, Read, Fractional) +newtype Position = Position Int deriving (Eq, Ord, Num, Enum, Show, Read) +newtype Identity = Identity Double deriving (Eq, Ord, Num, Show, Read) +newtype BlosumVal = BlosumVal { unBlosumVal :: Int } + deriving (Eq, Ord, Num, Enum, Show, Read) + +newtype ClusterMap = + ClusterMap { unClusterMap :: Map.Map Int (Seq.Seq FastaSequence) } + deriving (Eq, Ord, Show) +newtype ClusterFrequencyMap = + ClusterFrequencyMap + { unClusterFrequencyMap :: (Map.Map Position (Seq.Seq (AA, Frequency))) + } + deriving (Eq, Ord, Show) +newtype AAMap = AAMap + { unAAMap :: Map.Map AA (Map.Map AA Frequency) } + deriving (Eq, Ord, Show) +newtype BlockMap = BlockMap { unBlockMap :: AAMap } + deriving (Eq, Ord, Show) +newtype FrequencyMap = FrequencyMap { unFrequencyMap :: AAMap } + deriving (Eq, Ord, Show) +newtype Blosum = + Blosum { unBlosum :: (Map.Map AA (Map.Map AA BlosumVal)) } + deriving (Eq, Ord, Show) + +instance Monoid AAMap where + mempty = AAMap Map.empty + mappend (AAMap x) (AAMap y) = AAMap $ Map.unionWith (Map.unionWith (+)) x y diff --git a/src/Utility.hs b/src/Utility.hs new file mode 100644 --- /dev/null +++ b/src/Utility.hs @@ -0,0 +1,62 @@ +{- Utility +by Gregory Schwartz + +-- | Collects the functions pertaining to generic helpful functions +-} + +{-# LANGUAGE BangPatterns #-} +{-# LANGUAGE OverloadedStrings #-} + +module Utility + ( getSeq + , sortTuple + , nub' + , groupBlocks + , cutEnds + , sumMap + ) where + +-- Standard +import Data.List +import qualified Data.Set as Set +import qualified Data.Map.Strict as Map +import qualified Data.Sequence as Seq + +-- Cabal +import qualified Data.Text as T +import Data.Fasta.Text + +-- Local +import Types + +-- | Faster nub +nub' :: (Ord a) => [a] -> [a] +nub' = Set.toList . Set.fromList + +-- | Extract sequence from a fasta sequence +getSeq :: FastaSequence -> [AA] +getSeq = map AA . T.unpack . fastaSeq + +-- | Sort a tuple +sortTuple :: (Ord a) => (a, a) -> (a, a) +sortTuple t@(!x, !y) + | x <= y = t + | otherwise = (y, x) + +-- | Group together fasta entires by a field +groupBlocks :: Maybe Field -> [FastaSequence] -> [[FastaSequence]] +groupBlocks (Just field) = groupBy + (\x y -> getField field x == getField field y) +groupBlocks Nothing = (:[]) + +-- | Get a field from a fasta header +getField :: Field -> FastaSequence -> T.Text +getField (Field x) = (!! (x - 1)) . T.splitOn "|" . fastaHeader + +-- | Cut off the ends of a sequence +cutEnds :: Seq.Seq a -> Seq.Seq a +cutEnds = Seq.reverse . Seq.drop 1 . Seq.reverse . Seq.drop 1 + +-- | Sum up a map +sumMap :: (Ord a, Num b) => Map.Map a b -> b +sumMap = Map.foldl' (+) 0