Bio.RNAlienLibrary

This module contains functions for RNAlien

Documentation

module Bio.RNAlienData

createSessionID :: Maybe String -> IO String

Create session id for RNAlien

logMessage :: String -> String -> IO ()

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

modelConstructer :: StaticOptions -> ModelConstruction -> IO ModelConstruction

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

constructTaxonomyRecordsCSVTable :: ModelConstruction -> String

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

Used for passing progress to Alien server

setVerbose :: Verbosity -> Bool

logToolVersions :: String -> String -> IO ()

checkTools :: [String] -> String -> String -> IO (Either String String)

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

Run CMsearch

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

parse from input filePath

readCMSearches :: String -> IO (Either ParseError CMsearch)

parse from input filePath

compareCM :: String -> String -> String -> IO (Either String Double)

parseCMSearch :: String -> Either ParseError CMsearch

parse from input filePath

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

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

setInitialTaxId :: Maybe String -> String -> Maybe Int -> Sequence -> IO (Maybe Int)

evaluateConstructionResult :: StaticOptions -> ModelConstruction -> IO String

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

parse from input filePath

parseCMstat :: String -> Either ParseError CMstat

parse from input filePath

checkNCBIConnection :: IO (Either String String)

Check if alien can connect to NCBI

preprocessClustalForRNAz :: String -> String -> Int -> Double -> Double -> Bool -> IO (Either String (String, String))

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

Call for external preprocessClustalForRNAz

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

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

rnaZEvalOutput :: Either ParseError RNAz -> String

reformatFasta :: Sequence -> Sequence

checkTaxonomyRestriction :: Maybe String -> Maybe String

evaluePartitionTrimCMsearchHits :: Double -> [(CMsearch, (Sequence, Int, ByteString))] -> ([(CMsearch, (Sequence, Int, ByteString))], [(CMsearch, (Sequence, Int, ByteString))], [(CMsearch, (Sequence, Int, ByteString))])

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