diversity 0.2.0.5 → 0.3.0.0

raw patch · 10 files changed

+212/−210 lines, 10 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• diversity.cabal +4/−2
• src/src-exec/Main.hs +2/−2
• src/src-lib/Diversity/Diversity.hs +0/−67
• src/src-lib/Diversity/GenerateDiversity.hs +0/−42
• src/src-lib/Diversity/Print.hs +0/−73
• src/src-lib/Diversity/Types.hs +0/−24
• src/src-lib/Math/Diversity/Diversity.hs +67/−0
• src/src-lib/Math/Diversity/GenerateDiversity.hs +42/−0
• src/src-lib/Math/Diversity/Print.hs +73/−0
• src/src-lib/Math/Diversity/Types.hs +24/−0

@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/  name:                diversity-version:             0.2.0.5+version:             0.3.0.0 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@@ -16,12 +16,14 @@ cabal-version:       >=1.8  library+  ghc-options: -O2   hs-source-dirs:      src/src-lib-  exposed-modules:     Diversity.Types, Diversity.Diversity, Diversity.GenerateDiversity, Diversity.Print+  exposed-modules:     Math.Diversity.Types, Math.Diversity.Diversity, Math.Diversity.GenerateDiversity, Math.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+  ghc-options: -O2   -- Directories containing source files.   hs-source-dirs:      src/src-exec   main-is:             Main.hs

@@ -13,8 +13,8 @@ import Data.Fasta.String.Parse  -- Local-import Diversity.GenerateDiversity-import Diversity.Print+import Math.Diversity.GenerateDiversity+import Math.Diversity.Print  -- Command line arguments data Options = Options { inputLabel             :: String

@@ -1,67 +0,0 @@--- 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-

@@ -1,42 +0,0 @@--- 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 /= '.'

@@ -1,73 +0,0 @@--- 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-                 ]

@@ -1,24 +0,0 @@--- 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

@@ -0,0 +1,67 @@+-- Diversity module.+-- By G.W. Schwartz+--+{- | Collection of functions pertaining to finding the diversity of samples.+-}++module Math.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+

@@ -0,0 +1,42 @@+-- GenerateDiversity module.+-- By G.W. Schwartz+--+{- | Collection of functions for the collection of fragments for the+diversity calculations.+-}++module Math.Diversity.GenerateDiversity ( fragmentPos+                                        , generatePositionMap ) where++-- Built in+import qualified Data.Map as M+import Data.List+import Data.Fasta.String++-- Local+import Math.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 /= '.'

@@ -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 Math.Diversity.Print ( printDiversity+                            , printRarefaction+                            , printRarefactionCurve ) where++-- Built in+import Data.List+import qualified Data.Map as M++-- Local+import Math.Diversity.Types+import Math.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+                 ]

@@ -0,0 +1,24 @@+-- Types module.+-- By G.W. Schwartz+--+{- | Collects all application specific types.+-}++module Math.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