| Safe Haskell | Safe-Inferred |
|---|
Bio.ClustalParser
Description
Parse Clustal output For more information on Clustal tools consult: http://www.clustal.org/
- 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 :: String
- sequenceFormat :: String
- parametersOfInputSequences :: [SequenceParameters]
- pairwiseAlignmentSummaries :: [PairwiseAlignmentSummary]
- guideTreeFileName :: String
- groupNumber :: Int
- groupSummaries :: [GroupSummary]
- alignmentScore :: Int
- alignmentFileName :: String
- data SequenceParameters = SequenceParameters {
- inputSequenceIndex :: Int
- inputSequenceIdentifier :: String
- 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 :: String
- data ClustalAlignmentEntry = ClustalAlignmentEntry {
- entrySequenceIdentifier :: String
- entryAlignedSequence :: String
- data ClustalAlignmentSlice = ClustalAlignmentSlice {
- entrySlices :: [ClustalAlignmentEntrySlice]
- conservationTrackSlice :: String
- data ClustalAlignmentEntrySlice = ClustalAlignmentEntrySlice {
- entrySequenceSliceIdentifier :: String
- entryAlignedSliceSequence :: String
- spacerLength :: Int
- data StructuralClustalAlignment = StructuralClustalAlignment {
- structuralAlignmentEntries :: [ClustalAlignmentEntry]
- secondaryStructureTrack :: String
- energy :: Double
- data StructuralClustalAlignmentSlice = StructuralClustalAlignmentSlice {}
- data StructuralClustalAlignmentEntrySlice = StructuralClustalAlignmentEntrySlice {
- structuralEntrySequenceSliceIdentifier :: String
- structuralEntryAlignedSliceSequence :: String
Documentation
parseClustalAlignment :: String -> Either ParseError ClustalAlignmentSource
Parse Clustal alignment (.aln) from String
readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment)Source
Parse Clustal alignment (.aln) from filehandle
parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignmentSource
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 ClustalSummarySource
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
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Instances
| Eq ClustalSummary | |
| Show ClustalSummary |
data SequenceParameters Source
Constructors
| SequenceParameters | |
Fields
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Instances
| Eq SequenceParameters | |
| Show SequenceParameters |
data PairwiseAlignmentSummary Source
Constructors
| PairwiseAlignmentSummary | |
Fields
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Instances
data GroupSummary Source
Constructors
| GroupSummary | |
Fields
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Instances
| Eq GroupSummary | |
| Show GroupSummary |
data ClustalAlignment Source
Data structure for Clustal alignment format
Constructors
| ClustalAlignment | |
Fields
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Instances
| Eq ClustalAlignment | |
| Show ClustalAlignment |
data ClustalAlignmentEntry Source
Constructors
| ClustalAlignmentEntry | |
Fields
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Instances
data ClustalAlignmentSlice Source
Constructors
| ClustalAlignmentSlice | |
Fields
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Instances
data ClustalAlignmentEntrySlice Source
Constructors
| ClustalAlignmentEntrySlice | |
Fields
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Instances
data StructuralClustalAlignment Source
Data structure for structural Clustal alignment format
Constructors
| StructuralClustalAlignment | |
Fields
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Instances
data StructuralClustalAlignmentEntrySlice Source
Constructors
| StructuralClustalAlignmentEntrySlice | |
Fields
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Instances