Bio.Util

Documentation

wilson :: Double -> Int -> Int -> (Double, Double, Double)

Random useful stuff I didn't know where to put.

calculates the Wilson Score interval. If (l,m,h) = wilson c x n, then m is the binary proportion and (l,h) it's c-confidence interval for x positive examples out of n observations. c is typically something like 0.05.

invnormcdf :: (Ord a, Floating a) => a -> a

choose :: Integral a => a -> a -> a

Binomial coefficient: n choose k == n! / ((n-k)! k!)

estimateComplexity :: (Integral a, Floating b, Ord b) => a -> a -> Maybe b

Try to estimate complexity of a whole from a sample. Suppose we sampled total things and among those singles occured only once. How many different things are there?

Let the total number be m. The copy number follows a Poisson distribution with paramter lambda. Let z := e^{lambda}, then we have:

P( 0 ) = e^{-lambda} = 1/z P( 1 ) = lambda e^{-lambda} = ln z / z P(>=1) = 1 - e^{-lambda} = 1 - 1/z

singles = m ln z / z total = m (1 - 1/z)

D := totalsingles = (1 - 1z) * z / ln z f := z - 1 - D ln z = 0

To get z, we solve using Newton iteration and then substitute to get m:

dfdz = 1 - Dz z' := z - z (z - 1 - D ln z) / (z - D) m = singles * z /log z

It converges as long as the initial z is large enough, and 10D (in the line for zz below) appears to work well.

showNum :: Show a => a -> String

showOOM :: Double -> String

float2mini :: RealFloat a => a -> Word8

Conversion to 0.4.4 format minifloat: This minifloat fits into a byte. It has no sign, four bits of precision, and the range is from 0 to 63488, initially in steps of 1/8. Nice to store quality scores with reasonable precision and range.

mini2float :: Fractional a => Word8 -> a

Conversion from 0.4.4 format minifloat, see float2mini.

log1p :: (Floating a, Ord a) => a -> a

Computes log (1+x) to a relative precision of 10^-8 even for very small x. Stolen from http://www.johndcook.com/cpp_log_one_plus_x.html

expm1 :: (Floating a, Ord a) => a -> a

Computes exp x - 1 to a relative precision of 10^-10 even for very small x. Stolen from http://www.johndcook.com/cpp_expm1.html

phredplus :: Double -> Double -> Double infixl 3

Computes -10 * log_10 (10 ** (-x/10) + 10 ** (-y/10)) without losing precision. Used to add numbers on "the Phred scale", otherwise known as (deci-)bans.

phredminus :: Double -> Double -> Double infixl 3

Computes -10 * log_10 (10 ** (-x/10) - 10 ** (-y/10)) without losing precision. Used to subtract numbers on "the Phred scale", otherwise known as (deci-)bans.

phredsum :: [Double] -> Double

Computes -10 * log_10 (sum [10 ** (-x/10) | x <- xs]) without losing precision.

(<#>) :: Double -> Double -> Double infixl 3

phredconverse :: Double -> Double

Computes 1-p without leaving the "Phred scale"