{- | CGI program for calculating SNPs
output:
0) a pairwise check of equality
1) a table of variable positions
2) any other variable columns
3) ...
-}
import Network.CGI
import Columns
import Data.Char (isDigit)
-- | predefined polymorphic locations
snp_columns :: [Int]
snp_columns = [-21, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 --, 13I, 13II, 13III, 13IV, 13V, 13VI
, 14, 15, 16, 19, 62, 78, 89, 107, 117, 134, 145, 172
, 205, 207, 208, 214, 217, 218, 219, 250, 252, 265, 271, 272, 273, 289, 298
]
main :: IO ()
main = runCGI $ handleErrors cgiMain
cgiMain = do m <- getInput "alignment"
case m of
Just n -> let r = form ++ genResult n
in if r/=r then error "Aiieee" else output $ html r
Nothing -> output $ html form
-- replaces: alignCols . showCols
formatCols :: [String] -> [((Int,Char), [Char])] -> String
formatCols names cols = tabulate (hs:rows)
where (hs:rows) = showCols names cols
tabulate (h:rs) = table (tr th h ++ concatMap (tr td) rs)
table t = ""
th, td :: String -> String -> String
th t x = "| "++t++" | "
td t x = ""++t++" | "
tr :: (String -> String -> String) -> [String] -> String
tr c cs = ""++concat (zipWith c cs hs)++"
\n"
color x = case reads x of
[] -> "#FFFFFF"
(n,_):_ -> if n `elem` snp_columns then "#AFFFAF" else "#FFFFFF"
genResult s =
let (hs,ss) = unzip $ map splitLine $ drop 1 $ lines s
cols = transpose ss
in "Polymorphic columns
\n"++
(formatCols hs $ filterCols snp_columns $ enumerate (last ss) cols)++ "\n"
form = "Paste your alignment below:
\n" ++
"\n"
html c = "Alignment analyzer\n" ++ c ++"\n"