diversity 0.3.4.0 → 0.3.4.1

raw patch · 3 files changed

+14/−15 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• diversity.cabal +1/−1
• src/src-exec/Main.hs +2/−1
• src/src-lib/Math/Diversity/Diversity.hs +11/−13

@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/  name:                diversity-version:             0.3.4.0+version:             0.3.4.1 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

@@ -76,7 +76,8 @@          <> value "1 1"          <> help "The start point and interval of subsamples in the\                  \ rarefaction curve. For instance, '1 1' would be 1, 2, 3, ...\-                 \ '2 6' would be 2, 8, 14, ..." )+                 \ '2 6' would be 2, 8, 14, ... Note: input is a string so\+                 \ use quotations around the entry" )       <*> switch           ( long "fast-bin"          <> short 'f'

@@ -16,7 +16,6 @@ import Data.List import Data.Ratio import qualified Data.Set as Set-import qualified Data.Foldable as F import Numeric.SpecFunctions (choose) import Data.Function (on) @@ -77,7 +76,6 @@ getSampleContents = map (Set.fromList . map snd)                   . groupBy ((==) `on` fst)                   . sortBy (compare `on` fst)-                  . map (\(!x, !y) -> (x, y))  -- | Returns the rarefaction curve for each position in a list rarefactionSampleCurve :: (Ord a, Ord b)@@ -93,21 +91,21 @@         | t == 0       = (t, 0)         | t == t_total = (t, richness)         | otherwise    = (t, richness - inner t)-    inner t = ( \x -> if fastBin-                        then x / choose t_total t-                        else x )-            . F.sum-            . Set.map ( \s -> specialBinomial+    inner t     = ( \x -> if fastBin+                            then x / choose t_total t+                            else x )+                . sum+                . map ( \s -> specialBinomial                               fastBin                               (fromIntegral t_total)                               (numHave s samples)                               (fromIntegral t) )-            $ speciesList-    numHave s = sum . map (\x -> if Set.member s x then 1 else 0)-    richness = fromIntegral . Set.size $ speciesList-    speciesList = Set.fromList . map snd $ ls-    t_total = genericLength samples-    samples = getSampleContents ls+                $ speciesList+    numHave s   = sum . map (\x -> if Set.member s x then 1 else 0)+    richness    = genericLength speciesList+    speciesList = nub . map snd $ ls+    t_total     = genericLength samples+    samples     = getSampleContents ls  -- | Calculates the percent of the curve that is above 95% of height of the curve rarefactionViable :: [Double] -> Double