Bio.ClustalParser

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

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

Methods

(==) :: ClustalSummary -> ClustalSummary -> Bool

(/=) :: ClustalSummary -> ClustalSummary -> Bool

Show ClustalSummary

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

Methods

(==) :: SequenceParameters -> SequenceParameters -> Bool

(/=) :: SequenceParameters -> SequenceParameters -> Bool

Show SequenceParameters

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

Methods

(==) :: PairwiseAlignmentSummary -> PairwiseAlignmentSummary -> Bool

(/=) :: PairwiseAlignmentSummary -> PairwiseAlignmentSummary -> Bool

Show PairwiseAlignmentSummary

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

Methods

(==) :: GroupSummary -> GroupSummary -> Bool

(/=) :: GroupSummary -> GroupSummary -> Bool

Show GroupSummary

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

Methods

(==) :: ClustalAlignment -> ClustalAlignment -> Bool

(/=) :: ClustalAlignment -> ClustalAlignment -> Bool

Show ClustalAlignment

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

Methods

(==) :: ClustalAlignmentEntry -> ClustalAlignmentEntry -> Bool

(/=) :: ClustalAlignmentEntry -> ClustalAlignmentEntry -> Bool

Show ClustalAlignmentEntry

Methods

showsPrec :: Int -> ClustalAlignmentEntry -> ShowS

show :: ClustalAlignmentEntry -> String

showList :: [ClustalAlignmentEntry] -> ShowS

data ClustalAlignmentSlice

Constructors

ClustalAlignmentSlice

Fields

• entrySlices :: [ClustalAlignmentEntrySlice]
• conservationTrackSlice :: String

Instances

Eq ClustalAlignmentSlice

Methods

(==) :: ClustalAlignmentSlice -> ClustalAlignmentSlice -> Bool

(/=) :: ClustalAlignmentSlice -> ClustalAlignmentSlice -> Bool

Show ClustalAlignmentSlice

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

Methods

(==) :: ClustalAlignmentEntrySlice -> ClustalAlignmentEntrySlice -> Bool

(/=) :: ClustalAlignmentEntrySlice -> ClustalAlignmentEntrySlice -> Bool

Show ClustalAlignmentEntrySlice

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

Methods

(==) :: StructuralClustalAlignment -> StructuralClustalAlignment -> Bool

(/=) :: StructuralClustalAlignment -> StructuralClustalAlignment -> Bool

Show StructuralClustalAlignment

Methods

showsPrec :: Int -> StructuralClustalAlignment -> ShowS

show :: StructuralClustalAlignment -> String

showList :: [StructuralClustalAlignment] -> ShowS

data StructuralClustalAlignmentEntrySlice

Constructors

StructuralClustalAlignmentEntrySlice

Fields

• structuralEntrySequenceSliceIdentifier :: String
• structuralEntryAlignedSliceSequence :: String

Instances

Eq StructuralClustalAlignmentEntrySlice

Methods

(==) :: StructuralClustalAlignmentEntrySlice -> StructuralClustalAlignmentEntrySlice -> Bool

(/=) :: StructuralClustalAlignmentEntrySlice -> StructuralClustalAlignmentEntrySlice -> Bool

Show StructuralClustalAlignmentEntrySlice

Methods

showsPrec :: Int -> StructuralClustalAlignmentEntrySlice -> ShowS

show :: StructuralClustalAlignmentEntrySlice -> String

showList :: [StructuralClustalAlignmentEntrySlice] -> ShowS