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

Synopsis

Documentation

data RNAplexInteraction Source

Data structure for individual interaction between a target and query nucleic acid seqence

Constructors

RNAplexInteraction
Fields 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

Instances

Eq RNAplexInteraction
Show RNAplexInteraction

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

RNAplexInteraction
Fields 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

Instances

Eq RNAplexInteraction
Show RNAplexInteraction

data RNAzOutput Source

All elements of RNAz output are contained in this datatype

Constructors

RNAzOutput

Fields

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

Instances

Eq RNAzOutput
Show RNAzOutput

data RNAzResult Source

Datatype contains all result elements for each member of the input alignment

Constructors

RNAzResult
Fields header :: String resultSequence :: String dotBracket :: String minimumFreeEnergy :: Double zScore :: Double zscoreCalculationApproach :: Char

Instances

Eq RNAzResult
Show RNAzResult

data RNAzConsensus Source

Datatype contains all elements for the consenus result of input alignment

Constructors

RNAzConsensus
Fields consensusSequence :: String consensusDotBracket :: String

Instances

Eq RNAzConsensus
Show RNAzConsensus

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

RNAzOutput

Fields

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

Instances

Eq RNAzOutput
Show RNAzOutput

data RNAzResult Source

Datatype contains all result elements for each member of the input alignment

Constructors

RNAzResult
Fields header :: String resultSequence :: String dotBracket :: String minimumFreeEnergy :: Double zScore :: Double zscoreCalculationApproach :: Char

Instances

Eq RNAzResult
Show RNAzResult

data RNAzConsensus Source

Datatype contains all elements for the consenus result of input alignment

Constructors

RNAzConsensus
Fields consensusSequence :: String consensusDotBracket :: String

Instances

Eq RNAzConsensus
Show RNAzConsensus

data RNAfold Source

Data structure for individual interaction between a target and query nucleic acid seqence

Constructors

RNAfold
Fields sequenceIdentifier :: String foldSequence :: String foldSecondaryStructure :: String foldingEnergy :: Double

Instances

Eq RNAfold
Show RNAfold

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 RNAfold Source

Data structure for individual interaction between a target and query nucleic acid seqence

Constructors

RNAfold
Fields sequenceIdentifier :: String foldSequence :: String foldSecondaryStructure :: String foldingEnergy :: Double

Instances

Eq RNAfold
Show RNAfold

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
Fields alignmentConsensusSequence :: String alignmentConsensusDotBracket :: String alignmentConsensusMinimumFreeEnergy :: Double alignmentConsensusInitialMinimumFreeEnergy :: Double alignmentConsensusEnergyCovarianceContributions :: Double

Instances

Eq RNAalifoldOutput
Show RNAalifoldOutput

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
Fields alignmentConsensusSequence :: String alignmentConsensusDotBracket :: String alignmentConsensusMinimumFreeEnergy :: Double alignmentConsensusInitialMinimumFreeEnergy :: Double alignmentConsensusEnergyCovarianceContributions :: Double

Instances

Eq RNAalifoldOutput
Show RNAalifoldOutput

data RNAdistance Source

Data structure

Constructors

RNAdistance
Fields secondaryStructureDistance :: Int

Instances

Eq RNAdistance
Show RNAdistance

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 RNAdistance Source

Data structure

Constructors

RNAdistance
Fields secondaryStructureDistance :: Int

Instances

Eq RNAdistance
Show RNAdistance

data RNAupInteraction Source

Data structure for individual interaction between a target and query nucleic acid seqence, contains all (sub)-optimal interactions

Constructors

RNAupInteraction
Fields upQueryIdentifier :: String upTargetIdentifier :: String upInteractions :: [RNAupInteractionRegion]

Instances

Eq RNAupInteraction
Show RNAupInteraction

data RNAupInteractionRegion Source

Data structure for (sub-) optimal interaction region

Constructors

RNAupInteractionRegion
Fields 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

Instances

Eq RNAupInteractionRegion
Show RNAupInteractionRegion

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 upQueryIdentifier :: String upTargetIdentifier :: String upInteractions :: [RNAupInteractionRegion]

Instances

Eq RNAupInteraction
Show RNAupInteraction

data RNAupInteractionRegion Source

Data structure for (sub-) optimal interaction region

Constructors

RNAupInteractionRegion
Fields 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

Instances

Eq RNAupInteractionRegion
Show RNAupInteractionRegion