{-# LANGUAGE OverloadedStrings #-}
module Tests.Bed (tests) where
import Bio.Data.Bed
import Bio.Data.Bed.Types
import Bio.Data.Bed.Utils
import Bio.Utils.BitVector
import Control.Lens
import Conduit
import Data.Function (on)
import Data.List (sortBy, sort)
import qualified Data.Vector as V
import Test.Tasty
import Test.Tasty.HUnit
import qualified Data.HashMap.Strict as M
import Data.Ord
import Data.Maybe
tests :: TestTree
tests = testGroup "Test: Bio.Data.Bed"
[ testCase "sortBed" sortBedTest
, testCase "split" splitBedTest
, testCase "splitOverlapped" splitOverlappedTest
, testCase "intersectBed" intersectBedTest
, testCase "baseMap" baseMapTest
]
sortBedTest :: Assertion
sortBedTest = do beds <- readBed "tests/data/peaks.bed" :: IO [BED]
let (Sorted actual) = sortBed beds
expect <- fmap V.fromList $ readBed "tests/data/peaks.sorted.bed"
expect @=? actual
splitBedTest :: Assertion
splitBedTest = (s1', s2', s3') @=? (s1, s2, s3)
where
bed = asBed "chr1" 0 99
s1 = splitBedBySize 20 bed
s1' = map f [(0, 20), (20, 40), (40, 60), (60, 80)]
s2 = splitBedBySizeLeft 20 bed
s2' = map f [(0, 20), (20, 40), (40, 60), (60, 80), (80, 100)]
s3 = splitBedBySizeOverlap 20 10 bed
s3' = map f [ ( 0, 20), (10, 30), (20, 40), (30, 50), (40, 60)
, (50, 70), (60, 80), (70, 90), (80, 100) ]
f (a,b) = asBed "chr1" a b :: BED3
splitOverlappedTest :: Assertion
splitOverlappedTest = expect @=? result
where
input :: [BED3]
input = map (\(a,b) -> asBed "chr1" a b)
[ (0, 100)
, (10, 20)
, (50, 150)
, (120, 160)
, (155, 200)
, (155, 220)
]
expect = map (\((a,b), x) -> (asBed "chr1" a b, x))
[ ((0, 10), 1)
, ((10, 20), 2)
, ((20, 50), 1)
, ((50, 100), 2)
, ((100, 120), 1)
, ((120, 150), 2)
, ((150, 155), 1)
, ((155, 160), 3)
, ((160, 200), 2)
, ((200, 220), 1)
]
result = sortBy (compareBed `on` fst) $ splitOverlapped length input
intersectBedTest :: Assertion
intersectBedTest = do
expect <- readBed "tests/data/example_intersect_peaks.bed" :: IO [BED3]
peaks <- readBed "tests/data/peaks.bed" :: IO [BED3]
result <- runResourceT $ runConduit $ streamBed "tests/data/example.bed" .| intersectBed peaks .| sinkList
expect @=? result
baseMapTest :: Assertion
baseMapTest = do
BaseMap bv <- runResourceT $ runConduit $ streamBed "tests/data/example.bed" .|
baseMap [("chr1", 300000000)]
let res = M.lookupDefault undefined "chr1" $
fmap (map fst . filter snd . zip [0..] . toList) bv
expect <- runResourceT $ runConduit $ streamBed "tests/data/example.bed" .|
concatMapC f .| sinkList
sort expect @=? sort res
where
f :: BED -> Maybe Int
f bed = if bed^.chrom == "chr1"
then Just $ if fromJust (bed^.strand)
then bed^.chromStart
else bed^.chromEnd
else Nothing