Bio.RNAlienLibrary

This module contains functions for RNAlien

Documentation

module Bio.RNAlienData

createSessionID :: Maybe String -> IO String

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 -> IO ()

checkTools :: [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

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

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)

Call for external preprocessClustalForRNAz

rnaZEvalOutput :: Either ParseError RNAz -> String

reformatFasta :: Sequence -> Sequence

checkTaxonomyRestriction :: Maybe String -> Maybe String

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

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