SiteprofilesPhylobayesSpec.hs

{- |
Module      :  ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
Copyright   :  (c) Dominik Schrempf 2020
License     :  GPL-3.0-or-later

Maintainer  :  dominik.schrempf@gmail.com
Stability   :  unstable
Portability :  portable

Creation date: Wed Sep 18 09:51:35 2019.

-}

module ELynx.Import.MarkovProcess.SiteprofilesPhylobayesSpec
  ( spec
  )
where

import qualified Data.Vector.Storable          as V
import           Test.Hspec

import           ELynx.Tools

import           ELynx.Import.MarkovProcess.EDMModelPhylobayes
                                                ( EDMComponent )
import           ELynx.Import.MarkovProcess.SiteprofilesPhylobayes

fn :: FilePath
fn = "data/HSSPMany.siteprofiles"

getProfiles :: IO [EDMComponent]
getProfiles = parseFileWith siteprofiles fn

firstProfile :: V.Vector Double
firstProfile = V.fromList
  [ 0.0267009
  , 0.013874
  , 0.022432
  , 0.0440502
  , 0.0485174
  , 0.0407515
  , 0.0170806
  , 0.348043
  , 0.0371379
  , 0.0715536
  , 0.0454168
  , 0.0342213
  , 0.0146872
  , 0.0239681
  , 0.0768379
  , 0.0210387
  , 0.0123336
  , 0.0512678
  , 0.0149093
  , 0.0351776
  ]

spec :: Spec
spec =
  describe "import phylobayes siteprofiles"
    $ it "parses a text file with siteprofiles in phylobayes format"
    $ do
        profiles <- getProfiles
        length profiles `shouldBe` 701
        map fst profiles `shouldBe` replicate 701 1.0
        map (V.sum . snd) profiles
          `shouldSatisfy` nearlyEqListWith 1e-5 (replicate 701 1.0)
        snd (head profiles) `shouldBe` firstProfile