Safe Haskell	None
Language	Haskell98

Bio.ClustalParser

Description

Parse Clustal output For more information on Clustal tools consult: http://www.clustal.org/

Synopsis

parseClustalAlignment :: String -> Either ParseError ClustalAlignment
readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment)
parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment
readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment)
parseClustalSummary :: String -> Either ParseError ClustalSummary
readClustalSummary :: String -> IO (Either ParseError ClustalSummary)
data ClustalSummary = ClustalSummary {
- clustalw2version :: Text
- sequenceFormat :: Text
- parametersOfInputSequences :: [SequenceParameters]
- pairwiseAlignmentSummaries :: [PairwiseAlignmentSummary]
- guideTreeFileName :: Text
- groupNumber :: Int
- groupSummaries :: [GroupSummary]
- alignmentScore :: Int
- alignmentFileName :: Text
}
data SequenceParameters = SequenceParameters {
- inputSequenceIndex :: Int
- inputSequenceIdentifier :: Text
- inputSequenceLength :: Int
}
data PairwiseAlignmentSummary = PairwiseAlignmentSummary {
- firstSequenceIndex :: Int
- secondSequenceIndex :: Int
- pairwiseAlignmentScore :: Int
}
data GroupSummary = GroupSummary {
- alignmentGroupIndex :: Int
- numberOfAlignedSequences :: Maybe Int
- groupScore :: Maybe Int
}
data ClustalAlignment = ClustalAlignment {
- alignmentEntries :: [ClustalAlignmentEntry]
- conservationTrack :: Text
}
showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> Text -> String
showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> Text -> String
showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String
data ClustalAlignmentEntry = ClustalAlignmentEntry {
- entrySequenceIdentifier :: Text
- entryAlignedSequence :: Text
}
data ClustalAlignmentSlice = ClustalAlignmentSlice {
- entrySlices :: [ClustalAlignmentEntrySlice]
- conservationTrackSlice :: String
}
data ClustalAlignmentEntrySlice = ClustalAlignmentEntrySlice {
}
data StructuralClustalAlignment = StructuralClustalAlignment {
- structuralAlignmentEntries :: [ClustalAlignmentEntry]
- secondaryStructureTrack :: Text
- energy :: Double
}
data StructuralClustalAlignmentEntrySlice = StructuralClustalAlignmentEntrySlice {
- structuralEntrySequenceSliceIdentifier :: String
- structuralEntryAlignedSliceSequence :: String
}

Documentation

parseClustalAlignment :: String -> Either ParseError ClustalAlignment #

Parse Clustal alignment (.aln) from String

readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment) #

Parse Clustal alignment (.aln) from filehandle

parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment #

Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from String (as produced by mlocarna)

readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment) #

Parse Clustal alignment (.aln) with secondary structure in dot-bracket notation from filehandle (as produced by mlocarna)

parseClustalSummary :: String -> Either ParseError ClustalSummary #

Parse Clustal summary (printed to STDOUT) from String

readClustalSummary :: String -> IO (Either ParseError ClustalSummary) #

Parse Clustal summary (printed to STDOUT) from file

data ClustalSummary #

Data type for clustal summary, containing information about the alignment process, usually printed to STDOUT

Constructors

ClustalSummary
Fields clustalw2version :: Text sequenceFormat :: Text parametersOfInputSequences :: [SequenceParameters] pairwiseAlignmentSummaries :: [PairwiseAlignmentSummary] guideTreeFileName :: Text groupNumber :: Int groupSummaries :: [GroupSummary] alignmentScore :: Int alignmentFileName :: Text

Instances

Eq ClustalSummary #
Instance details Defined in Bio.ClustalData Methods (==) :: ClustalSummary -> ClustalSummary -> Bool # (/=) :: ClustalSummary -> ClustalSummary -> Bool #
Show ClustalSummary #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> ClustalSummary -> ShowS # show :: ClustalSummary -> String # showList :: [ClustalSummary] -> ShowS #

data SequenceParameters #

Constructors

SequenceParameters
Fields inputSequenceIndex :: Int inputSequenceIdentifier :: Text inputSequenceLength :: Int

Instances

Eq SequenceParameters #
Instance details Defined in Bio.ClustalData Methods (==) :: SequenceParameters -> SequenceParameters -> Bool # (/=) :: SequenceParameters -> SequenceParameters -> Bool #
Show SequenceParameters #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> SequenceParameters -> ShowS # show :: SequenceParameters -> String # showList :: [SequenceParameters] -> ShowS #

data PairwiseAlignmentSummary #

Constructors

PairwiseAlignmentSummary
Fields firstSequenceIndex :: Int secondSequenceIndex :: Int pairwiseAlignmentScore :: Int

Instances

Eq PairwiseAlignmentSummary #
Instance details Defined in Bio.ClustalData Methods (==) :: PairwiseAlignmentSummary -> PairwiseAlignmentSummary -> Bool # (/=) :: PairwiseAlignmentSummary -> PairwiseAlignmentSummary -> Bool #
Show PairwiseAlignmentSummary #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> PairwiseAlignmentSummary -> ShowS # show :: PairwiseAlignmentSummary -> String # showList :: [PairwiseAlignmentSummary] -> ShowS #

data GroupSummary #

Constructors

GroupSummary
Fields alignmentGroupIndex :: Int numberOfAlignedSequences :: Maybe Int groupScore :: Maybe Int

Instances

Eq GroupSummary #
Instance details Defined in Bio.ClustalData Methods (==) :: GroupSummary -> GroupSummary -> Bool # (/=) :: GroupSummary -> GroupSummary -> Bool #
Show GroupSummary #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> GroupSummary -> ShowS # show :: GroupSummary -> String # showList :: [GroupSummary] -> ShowS #

data ClustalAlignment #

Data structure for Clustal alignment format

Constructors

ClustalAlignment
Fields alignmentEntries :: [ClustalAlignmentEntry] conservationTrack :: Text

Instances

Eq ClustalAlignment #
Instance details Defined in Bio.ClustalData Methods (==) :: ClustalAlignment -> ClustalAlignment -> Bool # (/=) :: ClustalAlignment -> ClustalAlignment -> Bool #
Show ClustalAlignment #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> ClustalAlignment -> ShowS # show :: ClustalAlignment -> String # showList :: [ClustalAlignment] -> ShowS #

showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> Text -> String #

showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> Text -> String #

showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String #

data ClustalAlignmentEntry #

Constructors

ClustalAlignmentEntry
Fields entrySequenceIdentifier :: Text entryAlignedSequence :: Text

Instances

Eq ClustalAlignmentEntry #
Instance details Defined in Bio.ClustalData Methods (==) :: ClustalAlignmentEntry -> ClustalAlignmentEntry -> Bool # (/=) :: ClustalAlignmentEntry -> ClustalAlignmentEntry -> Bool #
Show ClustalAlignmentEntry #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> ClustalAlignmentEntry -> ShowS # show :: ClustalAlignmentEntry -> String # showList :: [ClustalAlignmentEntry] -> ShowS #

data ClustalAlignmentSlice #

Constructors

ClustalAlignmentSlice
Fields entrySlices :: [ClustalAlignmentEntrySlice] conservationTrackSlice :: String

Instances

Eq ClustalAlignmentSlice #
Instance details Defined in Bio.ClustalData Methods (==) :: ClustalAlignmentSlice -> ClustalAlignmentSlice -> Bool # (/=) :: ClustalAlignmentSlice -> ClustalAlignmentSlice -> Bool #
Show ClustalAlignmentSlice #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> ClustalAlignmentSlice -> ShowS # show :: ClustalAlignmentSlice -> String # showList :: [ClustalAlignmentSlice] -> ShowS #

data ClustalAlignmentEntrySlice #

Constructors

ClustalAlignmentEntrySlice
Fields entrySequenceSliceIdentifier :: String entryAlignedSliceSequence :: String spacerLength :: Int

Instances

Eq ClustalAlignmentEntrySlice #
Instance details Defined in Bio.ClustalData Methods (==) :: ClustalAlignmentEntrySlice -> ClustalAlignmentEntrySlice -> Bool # (/=) :: ClustalAlignmentEntrySlice -> ClustalAlignmentEntrySlice -> Bool #
Show ClustalAlignmentEntrySlice #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> ClustalAlignmentEntrySlice -> ShowS # show :: ClustalAlignmentEntrySlice -> String # showList :: [ClustalAlignmentEntrySlice] -> ShowS #

data StructuralClustalAlignment #

Data structure for structural Clustal alignment format

Constructors

StructuralClustalAlignment
Fields structuralAlignmentEntries :: [ClustalAlignmentEntry] secondaryStructureTrack :: Text energy :: Double

Instances

Eq StructuralClustalAlignment #
Instance details Defined in Bio.ClustalData Methods (==) :: StructuralClustalAlignment -> StructuralClustalAlignment -> Bool # (/=) :: StructuralClustalAlignment -> StructuralClustalAlignment -> Bool #
Show StructuralClustalAlignment #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> StructuralClustalAlignment -> ShowS # show :: StructuralClustalAlignment -> String # showList :: [StructuralClustalAlignment] -> ShowS #

data StructuralClustalAlignmentEntrySlice #

Constructors

StructuralClustalAlignmentEntrySlice
Fields structuralEntrySequenceSliceIdentifier :: String structuralEntryAlignedSliceSequence :: String

Instances

Eq StructuralClustalAlignmentEntrySlice #
Instance details Defined in Bio.ClustalData Methods (==) :: StructuralClustalAlignmentEntrySlice -> StructuralClustalAlignmentEntrySlice -> Bool # (/=) :: StructuralClustalAlignmentEntrySlice -> StructuralClustalAlignmentEntrySlice -> Bool #
Show StructuralClustalAlignmentEntrySlice #
Instance details Defined in Bio.ClustalData Methods showsPrec :: Int -> StructuralClustalAlignmentEntrySlice -> ShowS # show :: StructuralClustalAlignmentEntrySlice -> String # showList :: [StructuralClustalAlignmentEntrySlice] -> ShowS #