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 -> 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 :: Maybe String -> String -> Maybe Int -> Sequence -> 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 -> 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, ByteString))] -> ([(CMsearch, (Sequence, Int, ByteString))], [(CMsearch, (Sequence, Int, ByteString))], [(CMsearch, (Sequence, Int, ByteString))])
Documentation
module Bio.RNAlienData
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
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
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
rnaZEvalOutput :: Either ParseError RNAz -> String Source #
reformatFasta :: Sequence -> Sequence Source #
evaluePartitionTrimCMsearchHits :: Double -> [(CMsearch, (Sequence, Int, ByteString))] -> ([(CMsearch, (Sequence, Int, ByteString))], [(CMsearch, (Sequence, Int, ByteString))], [(CMsearch, (Sequence, Int, ByteString))]) Source #
Partitions sequences by containing a cmsearch hit and extracts the hit region as new sequence