I'm working on a Parsec parser to handle a somewhat complex data file format (and I have no control over this format).
I've made a lot of progress, but am currently stuck with the following.
I need to be able to parse a line somewhat like this:
4 0.123 1.452 0.667 * 3.460 149 - -
Semantically, the 4 is a nodeNum, the Floats and the * are negative log probabilities (so, * represents the negative log of probability zero). The 149 and the minus signs are really junk, which I can discard, but I need to at least make sure they don't break the parser.
Here's what I have so far:
This handles the "junk" I mentioned. It could probably be simpler, but it works by itself.
emAnnotationSet = (,,) <$> p_int <*>
(reqSpaces *> char '-') <*>
(reqSpaces *> char '-')
the nodeNum at the beginning of the line is handled by another parser that works and I need not get into.
The problem is in trying to pick out all the p_logProbs from the line, without consuming the digits at the beginning of the emAnnotationSet.
the parser for p_logProb looks like this:
p_logProb = liftA mkScore (lp <?> "logProb")
where lp = try dub <|> string "*"
dub = (++) <$> ((++) <$> many1 digit <*> string ".") <*> many1 digit
And finally, I try to separate the logProb entries from the trailing emAnnotationSet (which starts with an integer) as follows:
hmmMatchEmissions = optSpaces *> (V.fromList <$> sepBy p_logProb reqSpaces)
<* optSpaces <* emAnnotationSet <* eol
<?> "matchEmissions"
So, p_logProb will only succeed on a float that begins with digits, includes a decimal point, and then has further digits (this restriction is respected by the file format).
I'd hoped that the try in the p_logProb definition would avoid consuming the leading digits if it didn't parse the decimal and the rest, but this doesn't seem to work; Parsec still complains that it sees an unexpected space after the digits of that integer in the emAnnotationSet:
Left "hmmNode" (line 1, column 196):
unexpected " "
expecting logProb
column 196 corresponds to the space after the integer preceding the minus signs, so it's clear to me that the problem is that the p_logProb parser is consuming the integer. How can I fix this so the p_logProb parser uses lookahead correctly, thus leaving that input for the emAnnotationSet parser?
The integer which terminates the probabilities cannot be mistaken for a probability since it doesn't contain a decimal point. The lexeme combinator converts a parser into one that skips trailing spaces.
import Text.Parsec
import Text.Parsec.String
import Data.Char
import Control.Applicative ( (<$>), (<*>), (<$), (<*), (*>) )
fractional :: Fractional a => Parser a
fractional = try $ do
n <- fromIntegral <$> decimal
char '.'
f <- foldr (\d f -> (f + fromIntegral (digitToInt d))/10.0) 0.0 <$> many1 digit
return $ n + f
decimal :: Parser Int
decimal = foldl (\n d -> 10 * n + digitToInt d) 0 <$> many1 digit
lexeme :: Parser a -> Parser a
lexeme p = p <* skipMany (char ' ')
data Row = Row Int [Maybe Double]
deriving ( Show )
probability :: Fractional a => Parser (Maybe a)
probability = (Just <$> fractional) <|> (Nothing <$ char '*')
junk = lexeme decimal <* count 2 (lexeme $ char '-')
row :: Parser Row
row = Row <$> lexeme decimal <*> many1 (lexeme probability) <* junk
rows :: Parser [Row]
rows = spaces *> sepEndBy row (lexeme newline) <* eof
Usage:
*Main> parseTest rows "4 0.123 1.234 2.345 149 - -\n5 0.123 * 2.345 149 - -"
[Row 4 [Just 0.123,Just 1.234,Just 2.345],Row 5 [Just 0.123,Nothing,Just 2.345]]