Safe Haskell	Safe
Language	Haskell98

Bio.ClustalParser

Description

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

Synopsis

Documentation

parseClustalAlignment :: String -> Either ParseError ClustalAlignment Source

Parse Clustal alignment (.aln) from String

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

Parse Clustal alignment (.aln) from filehandle

parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment Source

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

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

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

parseClustalSummary :: String -> Either ParseError ClustalSummary Source

Parse Clustal summary (printed to STDOUT) from String

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

Parse Clustal summary (printed to STDOUT) from file

data ClustalSummary Source

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

Constructors

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

Instances

Eq ClustalSummary Source
Show ClustalSummary Source

data SequenceParameters Source

Constructors

SequenceParameters
Fields inputSequenceIndex :: Int inputSequenceIdentifier :: String inputSequenceLength :: Int

Instances

Eq SequenceParameters Source
Show SequenceParameters Source

data PairwiseAlignmentSummary Source

Constructors

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

Instances

Eq PairwiseAlignmentSummary Source
Show PairwiseAlignmentSummary Source

data GroupSummary Source

Constructors

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

Instances

Eq GroupSummary Source
Show GroupSummary Source

data ClustalAlignment Source

Data structure for Clustal alignment format

Constructors

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

Instances

Eq ClustalAlignment Source
Show ClustalAlignment Source

data ClustalAlignmentEntry Source

Constructors

ClustalAlignmentEntry
Fields entrySequenceIdentifier :: String entryAlignedSequence :: String

Instances

Eq ClustalAlignmentEntry Source
Show ClustalAlignmentEntry Source

data ClustalAlignmentSlice Source

Constructors

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

Instances

Eq ClustalAlignmentSlice Source
Show ClustalAlignmentSlice Source

data ClustalAlignmentEntrySlice Source

Constructors

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

Instances

Eq ClustalAlignmentEntrySlice Source
Show ClustalAlignmentEntrySlice Source

data StructuralClustalAlignment Source

Data structure for structural Clustal alignment format

Constructors

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

Instances

Eq StructuralClustalAlignment Source
Show StructuralClustalAlignment Source

data StructuralClustalAlignmentSlice Source

Constructors

StructuralClustalAlignmentSlice
Fields structuralEntrySlices :: [StructuralClustalAlignmentEntrySlice]

Instances

Eq StructuralClustalAlignmentSlice Source
Show StructuralClustalAlignmentSlice Source

data StructuralClustalAlignmentEntrySlice Source

Constructors

StructuralClustalAlignmentEntrySlice
Fields structuralEntrySequenceSliceIdentifier :: String structuralEntryAlignedSliceSequence :: String

Instances

Eq StructuralClustalAlignmentEntrySlice Source
Show StructuralClustalAlignmentEntrySlice Source