Shasta Python API documentation

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Class Assembler

class shasta.Assembler

__init__(self: shasta.Assembler, largeDataFileNamePrefix: str = 'Data/', createNew: bool = False, readRepresentation: SupportsInt = 1, largeDataPageSize: SupportsInt = 2097152) → None

Assembler constructor.

accessAlignmentCandidateTable(self: shasta.Assembler) → None

accessAlignmentCandidates(self: shasta.Assembler) → None

accessAlignmentData(self: shasta.Assembler) → None

accessAlignmentDataReadWrite(self: shasta.Assembler) → None

accessAssemblyGraphEdgeLists(self: shasta.Assembler) → None

accessAssemblyGraphEdges(self: shasta.Assembler) → None

accessAssemblyGraphOrientedReadsByEdge(self: shasta.Assembler) → None

accessAssemblyGraphSequences(self: shasta.Assembler) → None

accessAssemblyGraphVertices(self: shasta.Assembler) → None

accessCompressedAlignments(self: shasta.Assembler) → None

accessDisjointSetsHistogram(self: shasta.Assembler) → None

accessKmerChecker(self: shasta.Assembler) → None

accessKmers(self: shasta.Assembler) → None

accessMarkerGraphConsensus(self: shasta.Assembler) → None

accessMarkerGraphCoverageData(self: shasta.Assembler) → None

accessMarkerGraphEdgeMarkerIntervals(self: shasta.Assembler) → None

accessMarkerGraphEdges(self: shasta.Assembler, accessEdgesReadWrite: bool = False, accessConnectivityReadWrite: bool = False) → None

accessMarkerGraphReverseComplementEdge(self: shasta.Assembler) → None

accessMarkerGraphReverseComplementVertex(self: shasta.Assembler, readWriteAccess: bool = False) → None

accessMarkerGraphVertexRepeatCounts(self: shasta.Assembler) → None

accessMarkerGraphVertices(self: shasta.Assembler, readWriteAccess: bool = False) → None

accessMarkers(self: shasta.Assembler) → None

accessMode3Assembler(self: shasta.Assembler) → None

accessReadGraph(self: shasta.Assembler) → None

accessReadGraphReadWrite(self: shasta.Assembler) → None

accessSortedMarkers(self: shasta.Assembler) → bool

alignOrientedReads(self: shasta.Assembler, readId0: SupportsInt, strand0: SupportsInt, readId1: SupportsInt, strand1: SupportsInt, maxSkip: SupportsInt, maxDrift: SupportsInt, maxMarkerFrequency: SupportsInt) → None

alignOrientedReads1(self: shasta.Assembler, readId0: SupportsInt, strand0: SupportsInt, readId1: SupportsInt, strand1: SupportsInt, matchCount: SupportsInt, mismatchCount: SupportsInt, gapCount: SupportsInt) → None

alignOrientedReads4(self: shasta.Assembler, readId0: SupportsInt, strand0: SupportsInt, readId1: SupportsInt, strand1: SupportsInt, deltaX: SupportsInt, deltaY: SupportsInt, minEntryCountPerCell: SupportsInt, maxDistanceFromBoundary: SupportsInt, minAlignedMarkerCount: SupportsInt, minAlignedFraction: SupportsFloat, maxSkip: SupportsInt, maxDrift: SupportsInt, maxTrim: SupportsInt, maxBand: SupportsInt, matchScore: SupportsInt, mismatchScore: SupportsInt, gapScore: SupportsInt) → None

alignOverlappingOrientedReads(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt, maxSkip: SupportsInt, maxDrift: SupportsInt, maxMarkerFrequency: SupportsInt, minAlignedMarkerCount: SupportsInt, maxTrim: SupportsInt) → None

analyzeAlignmentMatrix(self: shasta.Assembler, readId0: SupportsInt, strand0: SupportsInt, readId1: SupportsInt, strand1: SupportsInt) → None

analyzeReadGraph(self: shasta.Assembler) → None

assemble(self: shasta.Assembler, threadCount: SupportsInt = 0, storeCoverageDataCsvLengthThreshold: SupportsInt = 0) → None

assembleAssemblyGraphEdge(self: shasta.Assembler, edgeId: SupportsInt, storeCoverageData: bool = True) → shasta::AssembledSegment

assembleMarkerGraphEdges(self: shasta.Assembler, threadCount: typing.SupportsInt = 0, markerGraphEdgeLengthThresholdForConsensus: typing.SupportsInt, storeCoverageData: bool, assembleAllEdges: bool) → None

assembleMarkerGraphVertices(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

checkMarkerGraphIsStrandSymmetric(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

cleanupDuplicateMarkers(self: shasta.Assembler, threadCount: typing.SupportsInt = 0, minCoverage: typing.SupportsInt, minCoveragePerStrand: typing.SupportsInt, duplicateMarkersPattern1Threshold: typing.SupportsFloat, pattern1CreateNewVertices: bool, pattern2CreateNewVertices: bool) → None

cleanupMarkerKmerIds(self: shasta.Assembler) → None

clusterMarkerGraphEdgeOrientedReads(self: shasta.Assembler, edgeId: SupportsInt, errorRateThreshold: SupportsFloat, debug: bool = False) → list[list[int]]

colorCompressedAssemblyGraph(self: shasta.Assembler, gfaId: str) → None

colorGfaBySimilarityToSegment(self: shasta.Assembler, segmentId: SupportsInt, minVertexCount: SupportsInt, minEdgeCount: SupportsInt) → None

colorGfaKeySegments(self: shasta.Assembler, fileName: str = 'Assembly-BothStrands-Color.csv') → None

colorGfaWithTwoReads(self: shasta.Assembler, readId0: SupportsInt, strand0: SupportsInt, readId1: SupportsInt, strand1: SupportsInt, fileName: str = 'Assembly-BothStrands-Color.csv') → None

computeAlignments(self: shasta.Assembler, arg0: shasta.AlignOptions, arg1: bool, arg2: SupportsInt) → None

computeAssemblyStatistics(self: shasta.Assembler) → None

computeMarkerGraphCoverageHistogram(self: shasta.Assembler) → None

computeMarkerGraphVerticesCoverageData(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

computeMarkerKmerIds(self: shasta.Assembler, arg0: SupportsInt) → None

computeReadGraphConnectedComponents(self: shasta.Assembler) → None

computeSortedMarkers(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

countKmers(self: shasta.Assembler, threadCount: SupportsInt = 0, globalFrequencyOverrideDirectory: str = '') → None

createAssemblyGraph2(self: shasta.Assembler, pruneLength: SupportsInt, mode2Options: shasta.Mode2AssemblyOptions, threadCount: SupportsInt = 0, debug: bool = False) → None

createAssemblyGraphEdges(self: shasta.Assembler) → None

createAssemblyGraphVertices(self: shasta.Assembler) → None

createCompressedAssemblyGraph(self: shasta.Assembler) → None

createMarkerGraphEdges(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

createMarkerGraphEdgesStrict(self: shasta.Assembler, minEdgeCoverage: SupportsInt, minEdgeCoveragePerStrand: SupportsInt, threadCount: SupportsInt = 0) → None

createMarkerGraphSecondaryEdges(self: shasta.Assembler, secondaryEdgeMaxSkip: SupportsInt, threadCount: SupportsInt = 0) → None

createMarkerGraphVertices(self: shasta.Assembler, minCoverage: SupportsInt, maxCoverage: SupportsInt, minCoveragePerStrand: SupportsInt, allowDuplicateMarkers: bool, peakFinderMinAreaFraction: SupportsFloat, peakFinderAreaStartIndex: SupportsInt, threadCount: SupportsInt = 0) → None

createPrimaryMarkerGraphEdges(self: shasta.Assembler, minPrimaryCoverage: SupportsInt, maxPrimaryCoverage: SupportsInt, threadCount: SupportsInt = 0) → None

createReadGraph(self: shasta.Assembler, maxAlignmentCount: SupportsInt, preferAlignedFraction: bool) → None

createReadGraph2(self: shasta.Assembler, maxAlignmentCount: SupportsInt, markerCountPercentile: SupportsFloat, alignedFractionPercentile: SupportsFloat, maxSkipPercentile: SupportsFloat, maxDriftPercentile: SupportsFloat, maxTrimPercentile: SupportsFloat) → None

createReadGraph3(self: shasta.Assembler, maxAlignmentCount: SupportsInt) → None

createReadGraph4(self: shasta.Assembler, maxAlignmentCount: SupportsInt) → None

createReadGraphUsingPseudoPaths(self: shasta.Assembler, matchScore: SupportsInt, mismatchScore: SupportsInt, gapScore: SupportsInt, mismatchSquareFactor: SupportsFloat, minScore: SupportsFloat, maxAlignmentCount: SupportsInt, threadCount: SupportsInt = 1) → None

detangle(self: shasta.Assembler) → None

detangle2(self: shasta.Assembler, diagonalReadCountMin: SupportsInt, offDiagonalReadCountMax: SupportsInt, offDiagonalRatio: SupportsFloat) → None

findAlignmentCandidatesLowHash0(self: shasta.Assembler, m: typing.SupportsInt, hashFraction: typing.SupportsFloat, minHashIterationCount: typing.SupportsInt, alignmentCandidatesPerRead: typing.SupportsFloat, log2MinHashBucketCount: typing.SupportsInt = 0, minBucketSize: typing.SupportsInt, maxBucketSize: typing.SupportsInt, minFrequency: typing.SupportsInt, threadCount: typing.SupportsInt = 0) → None

findMarkerGraphReverseComplementEdges(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

findMarkerGraphReverseComplementVertices(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

findMarkers(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

Find markers in reads.

flagChimericReads(self: shasta.Assembler, maxChimericReadDistance: SupportsInt, threadCount: SupportsInt = 0) → None

flagCrossStrandReadGraphEdges1(self: shasta.Assembler, maxDistance: SupportsInt, threadCount: SupportsInt = 0) → None

flagCrossStrandReadGraphEdges2(self: shasta.Assembler) → None

flagInconsistentAlignments(self: shasta.Assembler, triangleErrorThreshold: SupportsInt, leastSquareErrorThreshold: SupportsInt, leastSquareMaxDistance: SupportsInt, threadCount: SupportsInt = 0) → None

flagPalindromicReads(self: shasta.Assembler, maxSkip: SupportsInt, maxDrift: SupportsInt, maxMarkerFrequency: SupportsInt, alignedFractionThreshold: SupportsFloat, nearDiagonalFractionThreshold: SupportsFloat, deltaThreshold: SupportsInt, threadCount: SupportsInt = 0) → None

gatherOrientedReadsByAssemblyGraphEdge(self: shasta.Assembler, threadCount: SupportsInt = 0) → None

getAlignmentCandidates(self: shasta.Assembler) → list[shasta.OrientedReadPair]

getGlobalMarkerGraphVertex(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt, ordinal: SupportsInt) → int

getGlobalMarkerGraphVertexMarkers(self: shasta.Assembler, vertexId: SupportsInt) → list[tuple[int, int, int]]

getMarkerGraphMinCoverageUsed(self: shasta.Assembler) → int

getReads(self: shasta.Assembler) → shasta.Reads

histogramReadLength(self: shasta.Assembler, fileName: str = 'ReadLengthHistogram.csv') → None

Create a histogram of read length and write it to a csv file.

mode3Reassembly(self: shasta.Assembler, arg0: typing.SupportsInt, arg1: shasta::Mode3AssemblyOptions, arg2: bool) → None

pruneMarkerGraphStrongSubgraph(self: shasta.Assembler, iterationCount: SupportsInt) → None

readGraphClustering(self: shasta.Assembler) → None

removeAssemblyGraph(self: shasta.Assembler) → None

removeMarkerGraph(self: shasta.Assembler) → None

removeReadGraphBridges(self: shasta.Assembler, maxDistance: SupportsInt) → None

setMarkerGraphEdgeFlags(self: shasta.Assembler, wasRemovedByTransitiveReduction: SupportsInt, wasPruned: SupportsInt, isSuperBubbleEdge: SupportsInt, isLowCoverageCrossEdge: SupportsInt, wasAssembled: SupportsInt) → None

setupConsensusCaller(self: shasta.Assembler, arg0: str) → None

simplifyMarkerGraph(self: shasta.Assembler, maxLength: collections.abc.Sequence[SupportsInt], debug: bool = False) → None

splitMarkerGraphSecondaryEdges(self: shasta.Assembler, errorRateThreshold: SupportsFloat, minCoverage: SupportsInt, threadCount: SupportsInt = 0) → None

test(self: shasta.Assembler) → None

transitiveReduction(self: shasta.Assembler, lowCoverageThreshold: SupportsInt, highCoverageThreshold: SupportsInt, maxDistance: SupportsInt, edgeMarkerSkipThreshold: SupportsInt) → None

writeAlignmentCandidates(self: shasta.Assembler, useReadName: bool = False, verbose: bool = False) → None

writeAssemblyGraph(self: shasta.Assembler, arg0: str) → None

writeBadMarkerGraphVertices(self: shasta.Assembler) → None

writeFasta(self: shasta.Assembler, fileName: str) → None

writeGfa1(self: shasta.Assembler, fileName: str) → None

writeGfa1BothStrands(self: shasta.Assembler, fileName: str) → None

writeLocalAlignmentCandidateReads(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt, maxDistance: SupportsInt, allowChimericReads: bool, allowCrossStrandEdges: bool, allowInconsistentAlignmentEdges: bool) → None

writeLocalReadGraphReads(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt, maxDistance: SupportsInt, allowChimericReads: bool, allowCrossStrandEdges: bool, allowInconsistentAlignmentEdges: bool) → None

writeMarkers(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt, fileName: str) → None

Write the markers of an oriented read.

writeOrientedReadPath(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt, fileName: str = 'OrientedReadPath.csv') → None

writeOrientedReadsByAssemblyGraphEdge(self: shasta.Assembler) → None

writeOverlappingReads(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt, fileName: str = 'OverlappingReads.fasta') → None

Write in fasta format the reads that overlap a given read.

writeParallelMarkerGraphEdges(self: shasta.Assembler) → None

writePseudoPath(self: shasta.Assembler, readId: SupportsInt, strand: SupportsInt) → None

writeReadGraphEdges(self: shasta.Assembler, useReadName: bool = False) → None