Safe Haskell | None |
---|---|
Language | Haskell98 |
This module contains functions for RNAlien
- 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
- constructTaxonomyRecordsCSVTable :: ModelConstruction -> String
- resultSummary :: ModelConstruction -> StaticOptions -> IO ()
- setVerbose :: Verbosity -> Bool
- logToolVersions :: String -> IO ()
- checkTools :: [String] -> String -> IO (Either String String)
- systemCMsearch :: Int -> String -> String -> String -> String -> IO ExitCode
- readCMSearch :: String -> IO (Either ParseError CMsearch)
- compareCM :: String -> String -> String -> IO Double
- parseCMSearch :: String -> Either ParseError CMsearch
- cmSearchsubString :: Int -> Int -> String -> String
- setInitialTaxId :: Maybe String -> String -> Maybe Int -> Sequence -> IO (Maybe Int)
- evaluateConstructionResult :: StaticOptions -> Int -> IO String
- readCMstat :: String -> IO (Either ParseError CMstat)
- parseCMstat :: String -> Either ParseError CMstat
- checkNCBIConnection :: IO (Either String String)
- preprocessClustalForRNAz :: String -> String -> IO (Either String String)
- preprocessClustalForRNAzExternal :: String -> String -> IO (Either String String)
- 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))])
Documentation
module Bio.RNAlienData
logMessage :: String -> 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
setVerbose :: Verbosity -> Bool Source
logToolVersions :: String -> IO () Source
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
evaluateConstructionResult :: StaticOptions -> Int -> IO String Source
readCMstat :: String -> IO (Either ParseError CMstat) Source
parse from input filePath
parseCMstat :: String -> Either ParseError CMstat Source
parse from input filePath
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
reformatFasta :: Sequence -> Sequence Source
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