diversity (empty) → 0.2.0.5
raw patch · 8 files changed
+713/−0 lines, 8 filesdep +basedep +containersdep +diversitysetup-changed
Dependencies added: base, containers, diversity, fasta, math-functions, optparse-applicative, parsec, split
Files
- LICENSE +339/−0
- Setup.hs +2/−0
- diversity.cabal +29/−0
- src/src-exec/Main.hs +137/−0
- src/src-lib/Diversity/Diversity.hs +67/−0
- src/src-lib/Diversity/GenerateDiversity.hs +42/−0
- src/src-lib/Diversity/Print.hs +73/−0
- src/src-lib/Diversity/Types.hs +24/−0
+ LICENSE view
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+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ diversity.cabal view
@@ -0,0 +1,29 @@+-- Initial diversity.cabal generated by cabal init. For further +-- documentation, see http://haskell.org/cabal/users-guide/++name: diversity+version: 0.2.0.5+synopsis: Return the diversity at each position for all sequences in a fasta file+description: Find the diversity of a collection of entities, mainly for use with fasta sequences. Produces a binary which works on fasta files to find the diversity of any order and rarefaction curves for a sliding window across all positions in the sequences. To analyze just a collection of entities, just use the whole sequences and list flag.+homepage: https://github.com/GregorySchwartz/diversity+license: GPL-2+license-file: LICENSE+author: Gregory W. Schwartz+maintainer: gregory.schwartz@drexel.edu+-- copyright: +category: Bioinformatics+build-type: Simple+cabal-version: >=1.8++library+ hs-source-dirs: src/src-lib+ exposed-modules: Diversity.Types, Diversity.Diversity, Diversity.GenerateDiversity, Diversity.Print+ -- other-modules:+ build-depends: base >=4.6 && <4.8, containers >=0.5 && <0.6, split >=0.2 && <0.3, parsec >=3.1 && <4.0, fasta >=0.5.1.2 && <0.6, math-functions >=0.1 && <0.2++executable diversity+ -- Directories containing source files.+ hs-source-dirs: src/src-exec+ main-is: Main.hs+ -- other-modules: + build-depends: diversity, base >=4.6 && <4.8, optparse-applicative >=0.10 && <0.12, fasta >=0.5.1.2 && <0.6
+ src/src-exec/Main.hs view
@@ -0,0 +1,137 @@+-- Diversity+-- By G.W. Schwartz++{- | Takes a fasta file and return the diversity of a certain order and+window length (to split into fragments) by position.+-}++-- Built-in+import Data.List++-- Cabal+import Options.Applicative+import Data.Fasta.String.Parse++-- Local+import Diversity.GenerateDiversity+import Diversity.Print++-- Command line arguments+data Options = Options { inputLabel :: String+ , inputOrder :: Double+ , inputWindow :: Int+ , inputFasta :: String+ , fastBin :: Bool+ , removeN :: Bool+ , wholeSeq :: Bool+ , list :: Bool+ , outputRarefaction :: String+ , outputRarefactionCurve :: String+ , output :: String+ }++-- Command line options+options :: Parser Options+options = Options+ <$> strOption+ ( long "input-label"+ <> short 'l'+ <> metavar "LABEL"+ <> value ""+ <> help "The label for this particular dataset (to differentiate\+ \ the file in batch analyses)" )+ <*> option auto+ ( long "input-order"+ <> short 'r'+ <> metavar "[1]|INT"+ <> value 1+ <> help "The order of true diversity" )+ <*> option auto+ ( long "input-window"+ <> short 'w'+ <> metavar "[1]|INT"+ <> value 1+ <> help "The length of the sliding window for generating fragments" )+ <*> strOption+ ( long "input-fasta"+ <> short 'i'+ <> metavar "FILE"+ <> value ""+ <> help "The fasta file containing the germlines and clones" )+ <*> switch+ ( long "fast-bin"+ <> short 'f'+ <> help "Whether to use a much faster, but approximated, binomial\+ \ coefficient for the rarefaction analysis" )+ <*> switch+ ( long "remove-N"+ <> short 'n'+ <> help "Remove 'N' and 'n' characters" )+ <*> switch+ ( long "whole-sequence"+ <> short 'a'+ <> help "Ignore window length and only analyze the entire sequence for\+ \ diversity and rarefaction curves." )+ <*> switch+ ( long "list"+ <> short 'L'+ <> help "Analyze a diversity of species in a list separated by lines\+ \ instead of a fasta file" )+ <*> strOption+ ( long "output-rarefaction"+ <> short 'O'+ <> metavar "FILE"+ <> value ""+ <> help "The csv file containing the rarefaction values (the percent\+ \ of the rarefaction curve that is above 95% of the height of\+ \ the rarefaction curve)" )+ <*> strOption+ ( long "output-rarefaction-curve"+ <> short 'c'+ <> metavar "FILE"+ <> value ""+ <> help "The csv file containing the rarefaction curve" )+ <*> strOption+ ( long "output"+ <> short 'o'+ <> metavar "FILE"+ <> value ""+ <> help "The csv file containing the diversities at each position" )++generateDiversity :: Options -> IO ()+generateDiversity opts = do+ contentsFile <- readFile . inputFasta $ opts+ let lineIt = unlines . (:) ">" . intersperse ">" . lines+ contents = if (list opts) then lineIt contentsFile else contentsFile+ label = inputLabel opts+ order = inputOrder opts+ window = inputWindow opts+ nFlag = removeN opts+ whole = wholeSeq opts++ fastaListN = parseFasta contents+ fastaList = if nFlag then removeNs fastaListN else fastaListN+ positionMap = generatePositionMap whole window fastaList++ if (null . output $ opts)+ then return ()+ else writeFile (output opts)+ . printDiversity label order window+ $ positionMap+ if (null . outputRarefaction $ opts)+ then return ()+ else writeFile (outputRarefaction opts) $+ printRarefaction (fastBin opts) label window positionMap+ if (null . outputRarefactionCurve $ opts)+ then return ()+ else writeFile (outputRarefactionCurve opts) $+ printRarefactionCurve (fastBin opts) label window positionMap++main :: IO ()+main = execParser opts >>= generateDiversity+ where+ opts = info (helper <*> options)+ ( fullDesc+ <> progDesc "Return the diversity at each position for all sequences in a\+ \ fasta file"+ <> header "Diversity, Gregory W. Schwartz" )
+ src/src-lib/Diversity/Diversity.hs view
@@ -0,0 +1,67 @@+-- Diversity module.+-- By G.W. Schwartz+--+{- | Collection of functions pertaining to finding the diversity of samples.+-}++module Diversity.Diversity ( hamming+ , diversity+ , rarefactionCurve+ , rarefactionViable ) where++-- Built-in+import Data.List+import Data.Ratio+import Numeric.SpecFunctions (choose)++-- | Takes two strings, returns Hamming distance+hamming :: String -> String -> Int+hamming xs ys = length $ filter not $ zipWith (==) xs ys++-- | Returns the diversity of a list of things+diversity :: (Ord b) => Double -> [b] -> Double+diversity order sample+ | length sample == 0 = 0+ | order == 1 = exp . h $ speciesList+ | otherwise = (sum . map ((** order) . p_i) $ speciesList) ** pow+ where+ pow = 1 / (1 - order)+ h = negate . sum . map (\x -> (p_i x) * (log (p_i x)))+ p_i x = ((fromIntegral . length $ x) :: Double) /+ ((fromIntegral . length $ sample) :: Double)+ speciesList = group . sort $ sample++-- | Binomial for large numbers (slow but works for big numbers)+specialBinomial :: Bool -> Integer -> Integer -> Integer -> Double+specialBinomial False n_total g n = fromRational+ $ product [(n_total - g - n + 1)..(n_total - g)]+ % product [(n_total - n + 1)..n_total]+specialBinomial True n_total g n = choose+ (fromIntegral n_total - fromIntegral g)+ (fromIntegral n)++-- | Returns the rarefaction curve for each position in a list+rarefactionCurve :: (Eq a, Ord a) => Bool -> [a] -> [Double]+rarefactionCurve fastBin xs = map rarefact [1..n_total]+ where+ rarefact n+ | n == 0 = 0+ | n == 1 = 1+ | n == n_total = k+ | otherwise = k - inner n+ inner n = ( \x -> if fastBin+ then x / choose (fromIntegral n_total) (fromIntegral n)+ else x )+ . sum+ . map (\g -> specialBinomial fastBin n_total g n)+ $ grouped+ n_total = genericLength xs+ k = genericLength grouped+ grouped = map genericLength . group . sort $ xs++-- | Calculates the percent of the curve that is above 95% of height of the curve+rarefactionViable :: [Double] -> Double+rarefactionViable xs = (genericLength valid / genericLength xs) * 100+ where+ valid = dropWhile (< (0.95 * last xs)) xs+
+ src/src-lib/Diversity/GenerateDiversity.hs view
@@ -0,0 +1,42 @@+-- GenerateDiversity module.+-- By G.W. Schwartz+--+{- | Collection of functions for the collection of fragments for the+diversity calculations.+-}++module Diversity.GenerateDiversity ( fragmentPos+ , generatePositionMap ) where++-- Built in+import qualified Data.Map as M+import Data.List+import Data.Fasta.String++-- Local+import Diversity.Types++-- | Generates fragment list from string of "win" length. This version+-- differs from normal as it takes a tuple with the position as the first+-- entry+fragmentPos :: Bool -> Int -> [(Position, String)] -> [(Position, String)]+fragmentPos whole win xs | whole && null xs = error "Empty line in file!!"+ | whole = combine xs : []+ | length xs < win = []+ | otherwise = combine (take win xs)+ : fragmentPos whole win (tail xs)+ where+ combine = foldl1' (\(x, ys) (_, y) -> (x, ys ++ y))++-- | Generate the PositionMap from a list of FastaSequences+generatePositionMap :: Bool -> Window -> [FastaSequence] -> PositionMap+generatePositionMap whole win = M.fromListWith (++) . posSeqList+ where+ posSeqList = map toList . concatMap (\x -> fragmentPos whole win+ . map (\(p, f) -> (p, [f]))+ . filter (\(_, f) -> noGaps f)+ . zip [1..]+ . fastaSeq+ $ x)+ toList (x, y) = (x, [y])+ noGaps y = y /= '-' && y /= '.'
+ src/src-lib/Diversity/Print.hs view
@@ -0,0 +1,73 @@+-- Print module+-- By G.W. Schwartz+--+{- | Collection of functions for the printing of data (converting data+structures into strings for use with writing to output files).+-}++module Diversity.Print ( printDiversity+ , printRarefaction+ , printRarefactionCurve ) where++-- Built in+import Data.List+import qualified Data.Map as M++-- Local+import Diversity.Types+import Diversity.Diversity++-- Return the results of the diversity analysis in string form for saving+-- to a file+printDiversity :: Label -> Order -> Window -> PositionMap -> String+printDiversity label order window positionMap = header ++ body+ where+ header = "label,order,window,position,weight,diversity\n"+ body = unlines+ . map mapLine+ . M.toAscList+ $ positionMap+ mapLine (p, xs) = intercalate "," . line p $ xs+ line p xs = [ label+ , show order+ , show window+ , show p+ , show . length $ xs+ , show . diversity order $ xs+ ]++-- Return the results of the rarefaction analysis in string form for saving+-- to a file+printRarefaction :: Bool -> Label -> Window -> PositionMap -> String+printRarefaction fastBin label window positionMap = header ++ body+ where+ header = "label,window,position,weight,percent_above\n"+ body = unlines+ . map mapLine+ . M.toAscList+ $ positionMap+ mapLine (p, xs) = intercalate "," . line p $ xs+ line p xs = [ label+ , show window+ , show p+ , show . length $ xs+ , show . rarefactionViable . rarefactionCurve fastBin $ xs+ ]++-- Return the results of the rarefaction analysis of the entire curve in+-- string form for saving to a file+printRarefactionCurve :: Bool -> Label -> Window -> PositionMap -> String+printRarefactionCurve fastBin label window positionMap = header ++ body+ where+ header = "label,window,position,weight,curve\n"+ body = unlines+ . map mapLine+ . M.toAscList+ $ positionMap+ mapLine (p, xs) = intercalate "," . line p $ xs+ line p xs = [ label+ , show window+ , show p+ , show . length $ xs+ , intercalate "/" . map show . rarefactionCurve fastBin $ xs+ ]
+ src/src-lib/Diversity/Types.hs view
@@ -0,0 +1,24 @@+-- Types module.+-- By G.W. Schwartz+--+{- | Collects all application specific types.+-}++module Diversity.Types where++import qualified Data.Map as M++-- Basic+type Fragment = String+type Position = Int+type Diversity = Double+type Order = Double+type Label = String+type Window = Int++-- Advanced+-- | At each position we have a collection of fragments to find the+-- diversity of+type PositionMap = M.Map Position [Fragment]+-- | At each position we have a diversity+type DiversityMap = M.Map Position Diversity