RNAlien-1.0.0: Unsupervized construction of RNA family models

Safe HaskellNone
LanguageHaskell98

Bio.RNAlienLibrary

Description

This module contains functions for RNAlien

Synopsis

Documentation

logEither :: Show a => Either a b -> String -> IO () Source

modelConstructer :: StaticOptions -> ModelConstruction -> IO ModelConstruction Source

Initial RNA family model construction - generates iteration number, seed alignment and model

resultSummary :: ModelConstruction -> StaticOptions -> IO () Source

Used for passing progress to Alien server

systemCMsearch :: Int -> String -> String -> String -> String -> IO ExitCode Source

Run CMsearch

readCMSearch :: String -> IO (Either ParseError CMsearch) Source

parse from input filePath

parseCMSearch :: String -> Either ParseError CMsearch Source

parse from input filePath

cmSearchsubString :: Int -> Int -> String -> String Source

Extract a substring with coordinates from cmsearch, first nucleotide has index 1

readCMstat :: String -> IO (Either ParseError CMstat) Source

parse from input filePath

parseCMstat :: String -> Either ParseError CMstat Source

parse from input filePath

checkNCBIConnection :: IO (Either String String) Source

Check if alien can connect to NCBI

preprocessClustalForRNAz :: String -> String -> IO (Either String String) Source

RNAz can process 500 sequences at max. Using rnazSelectSeqs to isolate representative sample. rnazSelectSeqs only accepts - gap characters, alignment is reformatted accordingly.

preprocessClustalForRNAzExternal :: String -> String -> IO (Either String String) Source

Call for external preprocessClustalForRNAz

evaluePartitionTrimCMsearchHits :: Double -> [(CMsearch, (Sequence, Int, String, Char))] -> ([(CMsearch, (Sequence, Int, String, Char))], [(CMsearch, (Sequence, Int, String, Char))], [(CMsearch, (Sequence, Int, String, Char))]) Source

Partitions sequences by containing a cmsearch hit and extracts the hit region as new sequence