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 | SupportsIndex = 1, largeDataPageSize: SupportsInt | SupportsIndex = 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 | SupportsIndex, strand0: SupportsInt | SupportsIndex, readId1: SupportsInt | SupportsIndex, strand1: SupportsInt | SupportsIndex, maxSkip: SupportsInt | SupportsIndex, maxDrift: SupportsInt | SupportsIndex, maxMarkerFrequency: SupportsInt | SupportsIndex) → None

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

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

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

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

analyzeReadGraph(self: shasta.Assembler) → None

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

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

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

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

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

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

cleanupMarkerKmerIds(self: shasta.Assembler) → None

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

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

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

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

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

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

computeAssemblyStatistics(self: shasta.Assembler) → None

computeMarkerGraphCoverageHistogram(self: shasta.Assembler) → None

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

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

computeReadGraphConnectedComponents(self: shasta.Assembler) → None

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

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

createAssemblyGraph2(self: shasta.Assembler, pruneLength: SupportsInt | SupportsIndex, mode2Options: shasta.Mode2AssemblyOptions, threadCount: SupportsInt | SupportsIndex = 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 | SupportsIndex = 0) → None

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

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

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

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

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

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

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

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

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

detangle(self: shasta.Assembler) → None

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

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

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

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

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

Find markers in reads.

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

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

flagCrossStrandReadGraphEdges2(self: shasta.Assembler) → None

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

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

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

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

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

getGlobalMarkerGraphVertexMarkers(self: shasta.Assembler, vertexId: SupportsInt | SupportsIndex) → 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: SupportsInt | SupportsIndex, arg1: shasta::Mode3AssemblyOptions, arg2: bool) → None

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

readGraphClustering(self: shasta.Assembler) → None

removeAssemblyGraph(self: shasta.Assembler) → None

removeMarkerGraph(self: shasta.Assembler) → None

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

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

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

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

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

test(self: shasta.Assembler) → None

transitiveReduction(self: shasta.Assembler, lowCoverageThreshold: SupportsInt | SupportsIndex, highCoverageThreshold: SupportsInt | SupportsIndex, maxDistance: SupportsInt | SupportsIndex, edgeMarkerSkipThreshold: SupportsInt | SupportsIndex) → 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 | SupportsIndex, strand: SupportsInt | SupportsIndex, maxDistance: SupportsInt | SupportsIndex, allowChimericReads: bool, allowCrossStrandEdges: bool, allowInconsistentAlignmentEdges: bool) → None

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

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

Write the markers of an oriented read.

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

writeOrientedReadsByAssemblyGraphEdge(self: shasta.Assembler) → None

writeOverlappingReads(self: shasta.Assembler, readId: SupportsInt | SupportsIndex, strand: SupportsInt | SupportsIndex, 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 | SupportsIndex, strand: SupportsInt | SupportsIndex) → None

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