Shasta Python API documentation

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Class Assembler

class shasta.Assembler

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

Assembler constructor.

accessAlignmentCandidates(self: shasta.Assembler) → None

accessAlignmentData(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

accessKmers(self: shasta.Assembler) → None

accessMarkerGraphConsensus(self: shasta.Assembler) → None

accessMarkerGraphCoverageData(self: shasta.Assembler) → None

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

accessMarkerGraphReverseComplementEdge(self: shasta.Assembler) → None

accessMarkerGraphReverseComplementVertex(self: shasta.Assembler) → None

accessMarkerGraphVertexRepeatCounts(self: shasta.Assembler) → None

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

accessMarkers(self: shasta.Assembler) → None

accessReadGraph(self: shasta.Assembler) → None

accessReadGraphReadWrite(self: shasta.Assembler) → None

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

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

alignOrientedReads4(self: shasta.Assembler, readId0: int, strand0: int, readId1: int, strand1: int, m: int, deltaX: int, deltaY: int, matchScore: int, mismatchScore: int, gapScore: int) → None

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

alignPseudoPaths(self: shasta.Assembler, arg0: int, arg1: int, arg2: int, arg3: int) → None

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

analyzeReadGraph(self: shasta.Assembler) → None

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

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

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

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

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

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

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

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

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

computeAlignments(self: shasta.Assembler, alignmentMethod: int = 0, maxMarkerFrequency: int, maxSkip: int, maxDrift: int, minAlignedMarkerCount: int, minAlignedFraction: float, maxTrim: int, matchScore: int, mismatchScore: int, gapScore: int, downsamplingFactor: float, bandExtend: int, maxBand: int, suppressContainments: bool, storeAlignments: bool, threadCount: int = 0) → None

computeAssemblyStatistics(self: shasta.Assembler) → None

computeMarkerGraphCoverageHistogram(self: shasta.Assembler) → None

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

computeReadGraphConnectedComponents(self: shasta.Assembler, minComponentSize: int) → None

createAssemblyGraphEdges(self: shasta.Assembler) → None

createAssemblyGraphVertices(self: shasta.Assembler) → None

createCompressedAssemblyGraph(self: shasta.Assembler) → None

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

createMarkerGraphVertices(self: shasta.Assembler, alignMethod: int, maxMarkerFrequency: int, maxSkip: int, maxDrift: int, matchScore: int, mismatchScore: int, gapScore: int, downsamplingFactor: float, bandExtend: int, maxBand: int, minCoverage: int, maxCoverage: int, minCoveragePerStrand: int, peakFinderMinAreaFraction: float, peakFinderAreaStartIndex: int, threadCount: int = 0) → None

createReadGraph(self: shasta.Assembler, maxAlignmentCount: int, maxTrim: int) → None

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

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

detangle(self: shasta.Assembler) → None

detangle2(self: shasta.Assembler, diagonalReadCountMin: int, offDiagonalReadCountMax: int, offDiagonalRatio: float) → None

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

findAlignmentCandidatesLowHash1(self: shasta.Assembler, m: int, hashFraction: float, minHashIterationCount: int, log2MinHashBucketCount: int = 0, minBucketSize: int, maxBucketSize: int, minFrequency: int, threadCount: int = 0) → None

findAssemblyGraphBubbles(self: shasta.Assembler) → None

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

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

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

Find markers in reads.

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

flagCrossStrandReadGraphEdges(self: shasta.Assembler, maxDistance: int, threadCount: int = 0) → None

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

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

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

getGlobalMarkerGraphEdgeInformation(self: shasta.Assembler, vertexId0: int, vertexId1: int) → List[shasta.GlobalMarkerGraphEdgeInformation]

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

getGlobalMarkerGraphVertexChildren(self: shasta.Assembler, vertexId: int) → List[int]

getGlobalMarkerGraphVertexMarkers(self: shasta.Assembler, vertexId: int) → List[Tuple[int, int, int]]

getGlobalMarkerGraphVertexParents(self: shasta.Assembler, vertexId: int) → List[int]

getMarkers(self: shasta.Assembler, arg0: int, arg1: int) → List[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.

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

randomlySelectKmers(self: shasta.Assembler, k: int, probability: float, seed: int = 231) → None

readGraphClustering(self: shasta.Assembler) → None

refineMarkerGraph(self: shasta.Assembler, refineThreshold: int, threadCount: int = 0) → None

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

reverseTransitiveReduction(self: shasta.Assembler, lowCoverageThreshold: int, highCoverageThreshold: int, maxDistance: int) → None

selectKmers2(self: shasta.Assembler, k: int, markerDensity: float, seed: int = 231, enrichmentThreshold: float, threadCount: int = 0) → None

selectKmersBasedOnFrequency(self: shasta.Assembler, k: int, markerDensity: float, seed: int = 231, enrichmentThreshold: float, threadCount: int = 0) → None

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

simplifyMarkerGraph(self: shasta.Assembler, maxLength: List[int], debug: bool = False) → None

test(self: shasta.Assembler) → None

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

writeAlignmentCandidates(self: shasta.Assembler) → None

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

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

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

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

writeKmers(self: shasta.Assembler, fileName: str = 'Kmers.csv') → None

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

writeMarkerFrequency(self: shasta.Assembler) → None

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

Write the markers of an oriented read.

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

writeOrientedReadsByAssemblyGraphEdge(self: shasta.Assembler) → None

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

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

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