Safe Haskell	None
Language	Haskell2010

Biobase.RNAlien.Library

Description

This module contains functions for RNAlien

Synopsis

module Biobase.RNAlien.Types
createSessionID :: Maybe String -> IO String
logMessage :: String -> String -> IO ()
logEither :: Show a => Either a b -> String -> IO ()
modelConstructer :: StaticOptions -> ModelConstruction -> IO ModelConstruction
constructTaxonomyRecordsCSVTable :: ModelConstruction -> String
resultSummary :: ModelConstruction -> StaticOptions -> IO ()
setVerbose :: Verbosity -> Bool
logToolVersions :: String -> String -> IO ()
checkTools :: [String] -> String -> String -> IO (Either String String)
systemCMsearch :: Int -> String -> String -> String -> String -> IO ExitCode
readCMSearch :: String -> IO (Either ParseError CMsearch)
readCMSearches :: String -> IO (Either ParseError CMsearch)
compareCM :: String -> String -> String -> IO (Either String Double)
parseCMSearch :: String -> Either ParseError CMsearch
cmSearchsubString :: Int -> Int -> String -> String
setInitialTaxId :: Bool -> Int -> Maybe String -> String -> Maybe Int -> Fasta () () -> IO (Maybe Int)
evaluateConstructionResult :: StaticOptions -> ModelConstruction -> IO String
readCMstat :: String -> IO (Either ParseError CMstat)
parseCMstat :: String -> Either ParseError CMstat
checkNCBIConnection :: IO (Either String String)
preprocessClustalForRNAz :: String -> String -> Int -> Double -> Double -> Bool -> IO (Either String (String, String))
preprocessClustalForRNAzExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String, String))
preprocessClustalForRNAcodeExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String, String))
rnaZEvalOutput :: Either ParseError RNAz -> String
reformatFasta :: Fasta () () -> Fasta () ()
checkTaxonomyRestriction :: Maybe String -> Maybe String
evaluePartitionTrimCMsearchHits :: Double -> [(CMsearch, (Fasta () (), Int, ByteString))] -> ([(CMsearch, (Fasta () (), Int, ByteString))], [(CMsearch, (Fasta () (), Int, ByteString))], [(CMsearch, (Fasta () (), Int, ByteString))])
readFastaFile :: String -> IO [Fasta () ()]
writeFastaFile :: String -> [Fasta () ()] -> IO ()

Documentation

module Biobase.RNAlien.Types

createSessionID :: Maybe String -> IO String Source #

Create session id for RNAlien

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

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

constructTaxonomyRecordsCSVTable :: ModelConstruction -> String Source #

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

Used for passing progress to Alien server

setVerbose :: Verbosity -> Bool Source #

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

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

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

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

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

setInitialTaxId :: Bool -> Int -> Maybe String -> String -> Maybe Int -> Fasta () () -> IO (Maybe Int) Source #

evaluateConstructionResult :: StaticOptions -> ModelConstruction -> IO String Source #

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

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

rnaZEvalOutput :: Either ParseError RNAz -> String Source #

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

checkTaxonomyRestriction :: Maybe String -> Maybe String 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

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

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