Changelog

DNA Sequence as an Image

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module Main where
import Data.Array
import Data.Bits
import Data.List
import Data.Word
import qualified Codec.Compression.Zlib as Z
import qualified Data.ByteString.Lazy as B
 
be8 :: Word8 -> B.ByteString
be8 x = B.singleton x
 
be32 :: Word32 -> B.ByteString
be32 x = B.pack [fromIntegral (x `shiftR` sh) | sh <- [24,16,8,0]]
 
pack :: String -> B.ByteString
pack xs = B.pack $ map (fromIntegral.fromEnum) xs
 
unpack :: B.ByteString -> String
unpack xs = map (toEnum.fromIntegral) (B.unpack xs)
 
hdr, iHDR, iDAT, iEND :: B.ByteString
hdr = pack "\137\80\78\71\13\10\26\10"
iHDR = pack "IHDR"
iDAT = pack "IDAT"
iEND = pack "IEND"
 
chunk :: B.ByteString -> B.ByteString -> [B.ByteString]
chunk tag xs = [be32 (fromIntegral $ B.length xs), dat, be32 (crc dat)]
    where dat = B.append tag xs
 
png :: [[(Int,Int,Int,Int)]] -> B.ByteString
png dat = B.concat $ hdr : concat [ihdr, imgdat ,iend]
     where height = fromIntegral $ length dat
           width = fromIntegral $ length (head dat)
           ihdr = chunk iHDR $ B.concat 
                     [ be32 height
                     , be32 width
                     , be8 8   -- bits per sample (8 for r, 8 for g, 8 for b)
                     , be8 6   -- color type (2=rgb, 6=rgba)
                     , be8 0   -- compression method
                     , be8 0   -- filter method
                     , be8 0 ] -- interlace method
           imgdat = chunk iDAT (Z.compress imagedata)
           imagedata = B.concat $ map scanline dat
           iend = chunk iEND B.empty
 
scanline :: [(Int,Int,Int,Int)] -> B.ByteString
scanline dat = B.pack (0 : (map fromIntegral $ concatMap (\(r,g,b,a) -> [r,g,b,a]) dat))
 
crc :: B.ByteString -> Word32
crc xs = updateCrc 0xffffffff xs `xor` 0xffffffff
 
updateCrc :: Word32 -> B.ByteString -> Word32
updateCrc = B.foldl' crcStep
 
crcStep :: Word32 -> Word8 -> Word32
crcStep crc ch = (crcTab ! n) `xor` (crc `shiftR` 8)
    where n = fromIntegral (crc `xor` fromIntegral ch)
 
crcTab :: Array Word8 Word32
crcTab = listArray (0,255) $ flip map [0..255] (\n ->
    foldl' (\c k -> if c .&. 1 == 1
                      then 0xedb88320 `xor` (c `shiftR` 1)
                      else c `shiftR` 1) n [0..7])

eat :: B.ByteString -> (Int,Int,Int,Int)
eat seq = (process . B.head $ seq, process . B.head . B.drop 1 $ seq, process . B.head . B.drop 2 $ seq, process . B.head . B.drop 3 $ seq)
    where process x = ((fromIntegral x)-65)*6

main = do
    seq <- B.readFile "/home/bana/Downloads/rm2.fa"
    --B.writeFile "seq.txt" seq
    let xsiz = 800
        ysiz = 800
        dat = loop xsiz ysiz [[]] seq
            where   loop 0 0 img rseq = img
                    loop 0 y img rseq = loop xsiz (y-1) ([]:img) (B.drop 4 rseq)
                    loop x y (z:img) rseq = loop (x-1) y ((eat rseq:z):img) (B.drop 4 rseq)
        bsdat = png dat

    B.writeFile "testimg.png" bsdat
10:1: Error: Eta reduce
Found:
be8 x = B.singleton x
Why not:
be8 = B.singleton
48:24: Warning: Redundant $
Found:
0 :
(map fromIntegral $ concatMap (\ (r, g, b, a) -> [r, g, b, a]) dat)
Why not:
0 :
map fromIntegral (concatMap (\ (r, g, b, a) -> [r, g, b, a]) dat)
61:30: Error: Redundant flip
Found:
flip map [0 .. 255]
(\ n ->
foldl'
(\ c k ->
if c .&. 1 == 1 then 3988292384 `xor` (c `shiftR` 1) else
c `shiftR` 1)
n
[0 .. 7])
Why not:
map
(\ n ->
foldl'
(\ c k ->
if c .&. 1 == 1 then 3988292384 `xor` (c `shiftR` 1) else
c `shiftR` 1)
n
[0 .. 7])
[0 .. 255]
68:24: Warning: Redundant bracket
Found:
(fromIntegral x) - 65
Why not:
fromIntegral x - 65