diversity 0.3.4.1 → 0.3.5.0
raw patch · 2 files changed
+24/−14 lines, 2 filesPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
- diversity.cabal +1/−1
- src/src-exec/Main.hs +23/−13
diversity.cabal view
@@ -2,7 +2,7 @@ -- documentation, see http://haskell.org/cabal/users-guide/ name: diversity-version: 0.3.4.1+version: 0.3.5.0 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
src/src-exec/Main.hs view
@@ -29,6 +29,7 @@ , list :: Bool , sample :: Bool , rarefactionDF :: Bool+ , std :: Bool , outputRarefaction :: String , outputRarefactionCurve :: String , output :: String@@ -106,6 +107,11 @@ ( long "rarefaction-df" <> short 'd' <> help "Whether to output the rarefaction curve as a data frame" )+ <*> switch+ ( long "std"+ <> short 't'+ <> help "Whether to output to stdout or to a file if no file is\+ \ supplied" ) <*> strOption ( long "output-rarefaction" <> short 'O'@@ -129,7 +135,9 @@ generateDiversity :: Options -> IO () generateDiversity opts = do- contentsFile <- readFile . inputFasta $ opts+ contentsFile <- if (null . inputFasta $ opts)+ then getContents+ else readFile . inputFasta $ opts let lineIt = unlines . (:) ">" . intersperse ">" . lines contents = if (list opts) then lineIt contentsFile else contentsFile label = inputLabel opts@@ -149,14 +157,16 @@ window fastaList + howToOutput x = if std opts then putStrLn else writeFile x+ if (null . output $ opts) then return ()- else writeFile (output opts)+ else howToOutput (output opts) . printDiversity label order window $ positionMap if (null . outputRarefaction $ opts) then return ()- else writeFile (outputRarefaction opts)+ else howToOutput (outputRarefaction opts) $ printRarefaction (sample opts) (fastBin opts)@@ -167,16 +177,16 @@ positionMap if (null . outputRarefactionCurve $ opts) then return ()- else writeFile (outputRarefactionCurve opts) $- printRarefactionCurve- (rarefactionDF opts)- (sample opts)- (fastBin opts)- start- interval- label- window- positionMap+ else howToOutput (outputRarefactionCurve opts)+ $ printRarefactionCurve+ (rarefactionDF opts)+ (sample opts)+ (fastBin opts)+ start+ interval+ label+ window+ positionMap main :: IO () main = execParser opts >>= generateDiversity