| Safe Haskell | Safe-Inferred |
|---|---|
| Language | Haskell98 |
Bio.ViennaRNAParser
Description
Parsers for Programs from the Vienna RNA Package this libary is focused on Version > 2.0 For more information on the Vienna RNAPackage consult: http://www.tbi.univie.ac.at/~ivo/RNA/ or the homepage of the current maintainer: http://www.tbi.univie.ac.at/~ronny/RNA/index.html
- data RNAplexInteraction = RNAplexInteraction {
- targetIdentifier :: String
- queryIdentifier :: String
- plexSecondaryStructure :: String
- targetDuplexBegin :: Int
- targetDuplexEnd :: Int
- queryDuplexBegin :: Int
- queryDuplexEnd :: Int
- duplexEnergy :: Double
- duplexEnergyWithoutAccessiblity :: Maybe Double
- queryAccessiblity :: Maybe Double
- targetAccessibility :: Maybe Double
- parseRNAplex :: [Char] -> Either ParseError [RNAplexInteraction]
- readRNAplex :: String -> IO (Either ParseError [RNAplexInteraction])
- data RNAplexInteraction = RNAplexInteraction {
- targetIdentifier :: String
- queryIdentifier :: String
- plexSecondaryStructure :: String
- targetDuplexBegin :: Int
- targetDuplexEnd :: Int
- queryDuplexBegin :: Int
- queryDuplexEnd :: Int
- duplexEnergy :: Double
- duplexEnergyWithoutAccessiblity :: Maybe Double
- queryAccessiblity :: Maybe Double
- targetAccessibility :: Maybe Double
- data RNAzOutput = RNAzOutput {
- version :: String
- sequenceNumber :: Int
- columnNumber :: Int
- readingDirection :: String
- meanPairwiseIdentity :: Double
- shannonEntropy :: Double
- gcContent :: Double
- meanSingleSequenceMinimumFreeEnergy :: Double
- consensusMinimumFreeEnergy :: Double
- energyContribution :: Double
- covarianceContribution :: Double
- combinationsPair :: Double
- meanZScore :: Double
- structureConservationIndex :: Double
- backgroundModel :: String
- decisionModel :: String
- svmDecisionValue :: Double
- svmRNAClassProbability :: Double
- prediction :: String
- rnazResults :: [RNAzResult]
- rnazConsensus :: RNAzConsensus
- data RNAzResult = RNAzResult {}
- data RNAzConsensus = RNAzConsensus {}
- parseRNAz :: [Char] -> Either ParseError RNAzOutput
- readRNAz :: String -> IO (Either ParseError RNAzOutput)
- data RNAzOutput = RNAzOutput {
- version :: String
- sequenceNumber :: Int
- columnNumber :: Int
- readingDirection :: String
- meanPairwiseIdentity :: Double
- shannonEntropy :: Double
- gcContent :: Double
- meanSingleSequenceMinimumFreeEnergy :: Double
- consensusMinimumFreeEnergy :: Double
- energyContribution :: Double
- covarianceContribution :: Double
- combinationsPair :: Double
- meanZScore :: Double
- structureConservationIndex :: Double
- backgroundModel :: String
- decisionModel :: String
- svmDecisionValue :: Double
- svmRNAClassProbability :: Double
- prediction :: String
- rnazResults :: [RNAzResult]
- rnazConsensus :: RNAzConsensus
- data RNAzResult = RNAzResult {}
- data RNAzConsensus = RNAzConsensus {}
- data RNAfold = RNAfold {}
- parseRNAfold :: [Char] -> Either ParseError RNAfold
- readRNAfold :: String -> IO (Either ParseError RNAfold)
- data RNAfold = RNAfold {}
- data RNAalifoldOutput = RNAalifoldOutput {}
- parseRNAalifold :: [Char] -> Either ParseError RNAalifoldOutput
- readRNAalifold :: String -> IO (Either ParseError RNAalifoldOutput)
- data RNAalifoldOutput = RNAalifoldOutput {}
- data RNAdistance = RNAdistance {}
- parseRNAdistance :: [Char] -> Either ParseError RNAdistance
- readRNAdistance :: String -> IO (Either ParseError RNAdistance)
- data RNAdistance = RNAdistance {}
- data RNAupInteraction = RNAupInteraction {}
- data RNAupInteractionRegion = RNAupInteractionRegion {
- upSecondaryStructure :: String
- upQueryDuplexBegin :: Int
- upQueryDuplexEnd :: Int
- upTargetDuplexBegin :: Int
- upTargetDuplexEnd :: Int
- upDuplexEnergy :: Double
- upDuplexEnergyWithoutAccessiblity :: Maybe Double
- upQueryAccessiblity :: Maybe Double
- upTargetAccessibility :: Maybe Double
- upQuerySequence :: String
- upTargetSequence :: String
- upOutputFileName :: String
- parseRNAup :: [Char] -> Either ParseError [RNAupInteraction]
- readRNAup :: String -> IO (Either ParseError [RNAupInteraction])
- data RNAupInteraction = RNAupInteraction {}
- data RNAupInteractionRegion = RNAupInteractionRegion {
- upSecondaryStructure :: String
- upQueryDuplexBegin :: Int
- upQueryDuplexEnd :: Int
- upTargetDuplexBegin :: Int
- upTargetDuplexEnd :: Int
- upDuplexEnergy :: Double
- upDuplexEnergyWithoutAccessiblity :: Maybe Double
- upQueryAccessiblity :: Maybe Double
- upTargetAccessibility :: Maybe Double
- upQuerySequence :: String
- upTargetSequence :: String
- upOutputFileName :: String
Documentation
data RNAplexInteraction Source
Data structure for individual interaction between a target and query nucleic acid seqence
Constructors
Instances
parseRNAplex :: [Char] -> Either ParseError [RNAplexInteraction] Source
parse RNAplexOutput from input string
readRNAplex :: String -> IO (Either ParseError [RNAplexInteraction]) Source
parse from input filePath
data RNAplexInteraction Source
Data structure for individual interaction between a target and query nucleic acid seqence
Constructors
Instances
data RNAzOutput Source
All elements of RNAz output are contained in this datatype
Constructors
Instances
data RNAzResult Source
Datatype contains all result elements for each member of the input alignment
Constructors
| RNAzResult | |
Fields
| |
Instances
data RNAzConsensus Source
Datatype contains all elements for the consenus result of input alignment
Constructors
| RNAzConsensus | |
Fields | |
Instances
parseRNAz :: [Char] -> Either ParseError RNAzOutput Source
parse RNAzOutput from input string
readRNAz :: String -> IO (Either ParseError RNAzOutput) Source
parse from input filePath
data RNAzOutput Source
All elements of RNAz output are contained in this datatype
Constructors
Instances
data RNAzResult Source
Datatype contains all result elements for each member of the input alignment
Constructors
| RNAzResult | |
Fields
| |
Instances
data RNAzConsensus Source
Datatype contains all elements for the consenus result of input alignment
Constructors
| RNAzConsensus | |
Fields | |
Instances
Data structure for individual interaction between a target and query nucleic acid seqence
Constructors
| RNAfold | |
Fields | |
parseRNAfold :: [Char] -> Either ParseError RNAfold Source
parse RNAfold output from input string
readRNAfold :: String -> IO (Either ParseError RNAfold) Source
parse RNAfold output from input filePath
Data structure for individual interaction between a target and query nucleic acid seqence
Constructors
| RNAfold | |
Fields | |
data RNAalifoldOutput Source
Data structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequence
Constructors
| RNAalifoldOutput | |
Instances
parseRNAalifold :: [Char] -> Either ParseError RNAalifoldOutput Source
parse RNAalifold output from input string
readRNAalifold :: String -> IO (Either ParseError RNAalifoldOutput) Source
parse RNAalifold output from input filePath
data RNAalifoldOutput Source
Data structure corrsponds with alifoldoutput redirected to file. Output written directly to commandline also contains number of sequences and length of consensus sequence
Constructors
| RNAalifoldOutput | |
Instances
parseRNAdistance :: [Char] -> Either ParseError RNAdistance Source
parse RNAdistance output from input string
readRNAdistance :: String -> IO (Either ParseError RNAdistance) Source
parse RNAdistance output from input filePath
data RNAupInteraction Source
Data structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions
Constructors
| RNAupInteraction | |
Fields | |
Instances
data RNAupInteractionRegion Source
Data structure for (sub-) optimal interaction region
Constructors
parseRNAup :: [Char] -> Either ParseError [RNAupInteraction] Source
parse RNAupOutput from input string
readRNAup :: String -> IO (Either ParseError [RNAupInteraction]) Source
parse from input filePath
data RNAupInteraction Source
Data structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions
Constructors
| RNAupInteraction | |
Fields | |
Instances
data RNAupInteractionRegion Source
Data structure for (sub-) optimal interaction region
Constructors