RNAlien-1.6.0: Unsupervized construction of RNA family models

Safe HaskellNone
LanguageHaskell2010

Biobase.RNAlien.Library

Description

This module contains functions for RNAlien

Synopsis

Documentation

createSessionID :: Maybe String -> IO String Source #

Create session id for RNAlien

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

readCMSearches :: 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

preprocessClustalForRNAzExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String, String)) Source #

Call for external preprocessClustalForRNAz

preprocessClustalForRNAcodeExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String, String)) Source #

Call for external preprocessClustalForRNAcode - RNAcode additionally to RNAz requirements does not accept pipe,underscore, doublepoint symbols

reformatFasta :: Fasta () () -> Fasta () () Source #

evaluePartitionTrimCMsearchHits :: Double -> [(CMsearch, (Fasta () (), Int, ByteString))] -> ([(CMsearch, (Fasta () (), Int, ByteString))], [(CMsearch, (Fasta () (), Int, ByteString))], [(CMsearch, (Fasta () (), Int, ByteString))]) Source #

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

writeFastaFile :: String -> [Fasta () ()] -> IO () Source #