ClustalParser 1.1.3 → 1.1.4
raw patch · 5 files changed
+11/−10 lines, 5 filesPVP: major bump suggested
API removals or changes: PVP suggests a major version bump
API changes (from Hackage documentation)
- Bio.ClustalParser: alignmentEntries :: ClustalAlignment -> [ClustalAlignmentEntry]
- Bio.ClustalParser: alignmentFileName :: ClustalSummary -> String
- Bio.ClustalParser: alignmentGroupIndex :: GroupSummary -> Int
- Bio.ClustalParser: alignmentScore :: ClustalSummary -> Int
- Bio.ClustalParser: clustalw2version :: ClustalSummary -> String
- Bio.ClustalParser: conservationTrack :: ClustalAlignment -> String
- Bio.ClustalParser: conservationTrackSlice :: ClustalAlignmentSlice -> String
- Bio.ClustalParser: energy :: StructuralClustalAlignment -> Double
- Bio.ClustalParser: entryAlignedSequence :: ClustalAlignmentEntry -> String
- Bio.ClustalParser: entryAlignedSliceSequence :: ClustalAlignmentEntrySlice -> String
- Bio.ClustalParser: entrySequenceIdentifier :: ClustalAlignmentEntry -> String
- Bio.ClustalParser: entrySequenceSliceIdentifier :: ClustalAlignmentEntrySlice -> String
- Bio.ClustalParser: entrySlices :: ClustalAlignmentSlice -> [ClustalAlignmentEntrySlice]
- Bio.ClustalParser: firstSequenceIndex :: PairwiseAlignmentSummary -> Int
- Bio.ClustalParser: groupNumber :: ClustalSummary -> Int
- Bio.ClustalParser: groupScore :: GroupSummary -> Maybe Int
- Bio.ClustalParser: groupSummaries :: ClustalSummary -> [GroupSummary]
- Bio.ClustalParser: guideTreeFileName :: ClustalSummary -> String
- Bio.ClustalParser: inputSequenceIdentifier :: SequenceParameters -> String
- Bio.ClustalParser: inputSequenceIndex :: SequenceParameters -> Int
- Bio.ClustalParser: inputSequenceLength :: SequenceParameters -> Int
- Bio.ClustalParser: numberOfAlignedSequences :: GroupSummary -> Maybe Int
- Bio.ClustalParser: pairwiseAlignmentScore :: PairwiseAlignmentSummary -> Int
- Bio.ClustalParser: pairwiseAlignmentSummaries :: ClustalSummary -> [PairwiseAlignmentSummary]
- Bio.ClustalParser: parametersOfInputSequences :: ClustalSummary -> [SequenceParameters]
- Bio.ClustalParser: secondSequenceIndex :: PairwiseAlignmentSummary -> Int
- Bio.ClustalParser: secondaryStructureTrack :: StructuralClustalAlignment -> String
- Bio.ClustalParser: sequenceFormat :: ClustalSummary -> String
- Bio.ClustalParser: spacerLength :: ClustalAlignmentEntrySlice -> Int
- Bio.ClustalParser: structuralAlignmentEntries :: StructuralClustalAlignment -> [ClustalAlignmentEntry]
- Bio.ClustalParser: structuralEntryAlignedSliceSequence :: StructuralClustalAlignmentEntrySlice -> String
- Bio.ClustalParser: structuralEntrySequenceSliceIdentifier :: StructuralClustalAlignmentEntrySlice -> String
- Bio.ClustalParser: structuralEntrySlices :: StructuralClustalAlignmentSlice -> [StructuralClustalAlignmentEntrySlice]
+ Bio.ClustalParser: [alignmentEntries] :: ClustalAlignment -> [ClustalAlignmentEntry]
+ Bio.ClustalParser: [alignmentFileName] :: ClustalSummary -> String
+ Bio.ClustalParser: [alignmentGroupIndex] :: GroupSummary -> Int
+ Bio.ClustalParser: [alignmentScore] :: ClustalSummary -> Int
+ Bio.ClustalParser: [clustalw2version] :: ClustalSummary -> String
+ Bio.ClustalParser: [conservationTrackSlice] :: ClustalAlignmentSlice -> String
+ Bio.ClustalParser: [conservationTrack] :: ClustalAlignment -> String
+ Bio.ClustalParser: [energy] :: StructuralClustalAlignment -> Double
+ Bio.ClustalParser: [entryAlignedSequence] :: ClustalAlignmentEntry -> String
+ Bio.ClustalParser: [entryAlignedSliceSequence] :: ClustalAlignmentEntrySlice -> String
+ Bio.ClustalParser: [entrySequenceIdentifier] :: ClustalAlignmentEntry -> String
+ Bio.ClustalParser: [entrySequenceSliceIdentifier] :: ClustalAlignmentEntrySlice -> String
+ Bio.ClustalParser: [entrySlices] :: ClustalAlignmentSlice -> [ClustalAlignmentEntrySlice]
+ Bio.ClustalParser: [firstSequenceIndex] :: PairwiseAlignmentSummary -> Int
+ Bio.ClustalParser: [groupNumber] :: ClustalSummary -> Int
+ Bio.ClustalParser: [groupScore] :: GroupSummary -> Maybe Int
+ Bio.ClustalParser: [groupSummaries] :: ClustalSummary -> [GroupSummary]
+ Bio.ClustalParser: [guideTreeFileName] :: ClustalSummary -> String
+ Bio.ClustalParser: [inputSequenceIdentifier] :: SequenceParameters -> String
+ Bio.ClustalParser: [inputSequenceIndex] :: SequenceParameters -> Int
+ Bio.ClustalParser: [inputSequenceLength] :: SequenceParameters -> Int
+ Bio.ClustalParser: [numberOfAlignedSequences] :: GroupSummary -> Maybe Int
+ Bio.ClustalParser: [pairwiseAlignmentScore] :: PairwiseAlignmentSummary -> Int
+ Bio.ClustalParser: [pairwiseAlignmentSummaries] :: ClustalSummary -> [PairwiseAlignmentSummary]
+ Bio.ClustalParser: [parametersOfInputSequences] :: ClustalSummary -> [SequenceParameters]
+ Bio.ClustalParser: [secondSequenceIndex] :: PairwiseAlignmentSummary -> Int
+ Bio.ClustalParser: [secondaryStructureTrack] :: StructuralClustalAlignment -> String
+ Bio.ClustalParser: [sequenceFormat] :: ClustalSummary -> String
+ Bio.ClustalParser: [spacerLength] :: ClustalAlignmentEntrySlice -> Int
+ Bio.ClustalParser: [structuralAlignmentEntries] :: StructuralClustalAlignment -> [ClustalAlignmentEntry]
+ Bio.ClustalParser: [structuralEntryAlignedSliceSequence] :: StructuralClustalAlignmentEntrySlice -> String
+ Bio.ClustalParser: [structuralEntrySequenceSliceIdentifier] :: StructuralClustalAlignmentEntrySlice -> String
+ Bio.ClustalParser: [structuralEntrySlices] :: StructuralClustalAlignmentSlice -> [StructuralClustalAlignmentEntrySlice]
Files
- ClustalParser.cabal +3/−3
- ClustalParserTest.hs +2/−5
- changelog +2/−0
- src/Bio/ClustalData.hs +2/−1
- src/Bio/ClustalParser.hs +2/−1
ClustalParser.cabal view
@@ -5,7 +5,7 @@ -- PVP summary: +-+------- breaking API changes -- | | +----- non-breaking API additions -- | | | +--- code changes with no API change-version: 1.1.3+version: 1.1.4 synopsis: Libary for parsing Clustal tools output description: Currently contains parsers and datatypes for: clustalw2, clustalo, mlocarna, cmalign .@@ -36,8 +36,8 @@ source-repository this type: git- location: https://github.com/eggzilla/ClustalParser/tree/1.1.3- tag: 1.1.3+ location: https://github.com/eggzilla/ClustalParser/tree/1.1.4+ tag: 1.1.4 library -- Modules exported by the library.
ClustalParserTest.hs view
@@ -2,15 +2,12 @@ import System.Environment (getArgs) import Bio.ClustalParser-import Data.Either.Unwrap main :: IO () main = do args <- getArgs let input_file = (head args) -- read Clustal outputfile- parsedinput <- readClustalAlignment input_file- --parsedinput <- readStructuralClustalAlignment input_file- --print (entrySequenceIdentifier (head (structuralAlignmentEntries(fromRight parsedinput))))- print (fromRight parsedinput)+ parsedinput <- readStructuralClustalAlignment input_file+ print parsedinput
changelog view
@@ -1,4 +1,6 @@ -*-change-log-*-+1.1.4 Florian Eggenhofer <egg@cs.uni-freiburg.de> 30. May 2016+ * Fixed a bug in output of clustal alignments with sequence length of 60 1.1.3 Florian Eggenhofer <florian.eggenhofer@univie.ac.at> 4. July 2015 * Nucleotide sequences are now parsed by a unified function in line with IUPAC nucleotide code
src/Bio/ClustalData.hs view
@@ -63,7 +63,8 @@ showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> String -> String showAlignment totalSequenceLength longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack | totalSequenceLength == 0 = [] - | currentWindowPosition <= totalSequenceLength = showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack ++ (showAlignment totalSequenceLength longestSequenceIdLength (currentWindowPosition + 60) _alignmentEntries _conservationTrack)+ | currentWindowPosition < totalSequenceLength = showAlignmentBlock longestSequenceIdLength currentWindowPosition _alignmentEntries _conservationTrack ++ (showAlignment totalSequenceLength longestSequenceIdLength (currentWindowPosition + 60) _alignmentEntries _conservationTrack)+ | currentWindowPosition == totalSequenceLength = [] | otherwise = "" showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> String -> String
src/Bio/ClustalParser.hs view
@@ -114,8 +114,9 @@ -- | Parse the input as ClustalAlignment datatype genParserClustalAlignment :: GenParser Char st ClustalAlignment genParserClustalAlignment = do+ string "CLUSTAL" many1 (noneOf "\n")- many1 newline+ many1 (try newline) alignmentSlices <- many1 (try genParserClustalAlignmentSlice) eof return (mergealignmentSlices alignmentSlices)