1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
|
{-# LANGUAGE OverloadedStrings #-}
module Genome
(
genome
) where
import Control.Applicative
import Test.Tasty.Bench
import Data.ByteString (ByteString)
import qualified Data.ByteString.Char8 as B8
import qualified Data.ByteString.Lazy.Char8 as L8
import Data.Attoparsec.ByteString.Char8 as B
import qualified Data.Attoparsec.ByteString.Lazy as BL
import Data.Text (Text)
import qualified Data.Text as T
import qualified Data.Text.Lazy as TL
import Data.Attoparsec.Text as T
import qualified Data.Attoparsec.Text.Lazy as TL
import Common (rechunkBS, rechunkT)
genome :: Benchmark
genome = bgroup "genome" [
bgroup "bytestring" [
bench "s" $ nf (map (B.parse searchBS)) (B8.tails geneB)
, bench "l" $ nf (map (BL.parse searchBS)) (L8.tails geneBL)
, bgroup "CI" [
bench "s" $ nf (map (B.parse searchBSCI)) (B8.tails geneB)
, bench "l" $ nf (map (BL.parse searchBSCI)) (L8.tails geneBL)
]
]
, bgroup "text" [
bench "s" $ nf (map (T.parse searchT)) (T.tails geneT)
, bench "l" $ nf (map (TL.parse searchT)) (TL.tails geneTL)
, bgroup "CI" [
bench "s" $ nf (map (T.parse searchTCI)) (T.tails geneT)
, bench "l" $ nf (map (TL.parse searchTCI)) (TL.tails geneTL)
]
]
]
where geneB = B8.pack gene
geneBL = rechunkBS 4 geneB
geneT = T.pack gene
geneTL = rechunkT 4 geneT
searchBS :: B.Parser ByteString
searchBS = "caac" *> ("aaca" <|> "aact")
searchBSCI :: B.Parser ByteString
searchBSCI = B.stringCI "CAAC" *> (B.stringCI "AACA" <|> B.stringCI "AACT")
searchT :: T.Parser Text
searchT = "caac" *> ("aaca" <|> "aact")
searchTCI :: T.Parser Text
searchTCI = T.asciiCI "CAAC" *> (T.asciiCI "AACA" <|> T.asciiCI "AACT")
-- Dictyostelium discoideum developmental protein DG1094 (gacT) gene,
-- partial cds. http://www.ncbi.nlm.nih.gov/nuccore/AF081586.1
gene :: String
gene = "atcgatttagaaagatacaaagatagaaccatcaataataaacaagagaagagagcaagt\
\agagatattaataaagagattgaaagagagattgaaaagaagagattatcaccaagagaa\
\agattaaatttatttggtctttcttcctcatcttcatcagtgaattcaacattaacaaga\
\tctacagcaaatattatctctacaatagacggtagtggaggtagtaatcgtaatagtaaa\
\aattatggtaatggctcatcctcctcctcaaatagaagatatagtaatactattaatcaa\
\caattacaaatgcaattacaacaacttcaaatccaacaacaacaatatcaacaaactcaa\
\caatctcaaataccattacaatatcaacaacaacaacagcaacaacaacaacaaaccact\
\acaactacaactacatcaagtggtagtaatagattctcttcaaatagatataaaccagtt\
\gatcttacacaatcatcttcaaactttcgttattcacgtgaaatttatgatgatgattat\
\tattcaaataataatttaatgatgtttggtaatgagcaaccaaatcaaacaccaatttct\
\gtatcatcttcatctgcattcacacgtcaaagatctcaaagttgctttgaaccagagaat\
\cttgtattgctacaacaacaatatcaacaatatcaacaacaacaacaacaacaacaacaa\
\attccattccaagcaaatccacaatatagtaatgctgttattgaacaaaaattggatcaa\
\attagagataccattaataatttacatagagataaccgagtctctaga"
|
