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