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#!/usr/bin/python3
"""
This runs a portion of Mode 2 assembly.
It starts at read graph creation, so the alignments must be available.
It then creates the marker graph using the Mode 1/2 protocol
(strict edge creation + creation of secondary edges).
Finally, it assembles all of the marker graph vertices and edges.
"""
import shasta
import GetConfig
import ast
import os
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessKmers()
a.accessMarkers()
a.accessAlignmentDataReadWrite()
a.accessCompressedAlignments()
a.setupConsensusCaller(config['Assembly']['consensusCaller'])
# Create the read graph.
readGraphCreationMethod = int(config['ReadGraph']['creationMethod'])
if readGraphCreationMethod == 0:
a.createReadGraph(
maxAlignmentCount = int(config['ReadGraph']['maxAlignmentCount']))
elif readGraphCreationMethod == 2:
a.createReadGraph2(
maxAlignmentCount = int(config['ReadGraph']['maxAlignmentCount']),
markerCountPercentile = float(config['ReadGraph']['markerCountPercentile']),
alignedFractionPercentile = float(config['ReadGraph']['alignedFractionPercentile']),
maxSkipPercentile = float(config['ReadGraph']['maxSkipPercentile']),
maxDriftPercentile = float(config['ReadGraph']['maxDriftPercentile']),
maxTrimPercentile = float(config['ReadGraph']['maxTrimPercentile']))
else:
raise ValueError('Invalid value for --ReadGraph.creationMethod.')
strandSeparationMethod = int(config['ReadGraph']['strandSeparationMethod'])
# Limited strand separation in the read graph.
if strandSeparationMethod==1:
a.flagCrossStrandReadGraphEdges1(
maxDistance = int(config['ReadGraph']['crossStrandMaxDistance']))
a.flagChimericReads(
maxChimericReadDistance = int(config['ReadGraph']['maxChimericReadDistance']))
# Flag inconsistent alignments, if requested.
flagInconsistentAlignments = ast.literal_eval(config['ReadGraph']['flagInconsistentAlignments'])
if flagInconsistentAlignments:
a.flagInconsistentAlignments(
triangleErrorThreshold = config['ReadGraph']['flagInconsistentAlignmentsTriangleErrorThreshold'],
leastSquareErrorThreshold = config['ReadGraph']['flagInconsistentAlignmentsLeastSquareErrorThreshold'],
leastSquareMaxDistance = config['ReadGraph']['flagInconsistentAlignmentsLeastSquareMaxDistance'])
# Strict strand separation in the read graph.
if strandSeparationMethod == 2:
a.flagCrossStrandReadGraphEdges2()
# Compute connected components of the read graph.
# These are currently not used.
if not strandSeparationMethod == 2:
a.computeReadGraphConnectedComponents()
# Create the marker graph using strict edge creation.
a.createMarkerGraphVertices(
minCoverage = int(config['MarkerGraph']['minCoverage']),
maxCoverage = int(config['MarkerGraph']['maxCoverage']),
minCoveragePerStrand = int(config['MarkerGraph']['minCoveragePerStrand']),
allowDuplicateMarkers = ast.literal_eval(config['MarkerGraph']['allowDuplicateMarkers']),
peakFinderMinAreaFraction = float(config['MarkerGraph']['peakFinder.minAreaFraction']),
peakFinderAreaStartIndex = int(config['MarkerGraph']['peakFinder.areaStartIndex']))
a.findMarkerGraphReverseComplementVertices()
a.createMarkerGraphEdgesStrict(
minEdgeCoverage = int(config['MarkerGraph']['minEdgeCoverage']),
minEdgeCoveragePerStrand = int(config['MarkerGraph']['minEdgeCoveragePerStrand']))
a.findMarkerGraphReverseComplementEdges()
a.computeMarkerGraphCoverageHistogram()
# Add secondary edges.
a.createMarkerGraphSecondaryEdges(
secondaryEdgeMaxSkip = int(config['MarkerGraph']['secondaryEdges.maxSkip']))
a.splitMarkerGraphSecondaryEdges(
errorRateThreshold = float(config['MarkerGraph']['secondaryEdges.split.errorRateThreshold']),
minCoverage = int(config['MarkerGraph']['secondaryEdges.split.minCoverage']))
# Assembler all marker graph vertices and edges.
a.assembleMarkerGraphVertices()
a.assembleMarkerGraphEdges(
markerGraphEdgeLengthThresholdForConsensus =
int(config['Assembly']['markerGraphEdgeLengthThresholdForConsensus']),
storeCoverageData = ast.literal_eval(config['Assembly']['storeCoverageData']),
assembleAllEdges = True)
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