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#!/usr/bin/python3
"""
This run the final portion of Mode 2 assembly.
"""
import ast
import argparse
import shasta
import GetConfig
parser = argparse.ArgumentParser()
parser.add_argument('--debug', action='store_true')
parser.add_argument('--no-debug', action='store_false')
parser.set_defaults(debug=False)
arguments = parser.parse_args()
debug = arguments.debug
config = GetConfig.getConfig()
shasta.openPerformanceLog('Mode2Assembly-B.log')
a = shasta.Assembler()
a.accessMarkers()
a.accessMarkerGraphVertices()
a.accessMarkerGraphReverseComplementVertex()
a.accessMarkerGraphEdges(accessEdgesReadWrite = True)
a.accessMarkerGraphReverseComplementEdge()
a.accessMarkerGraphConsensus()
# Fill in the Mode2Assemblyoptions.
mode2Options = shasta.Mode2AssemblyOptions();
mode2Options.strongBranchThreshold = int(config['Assembly']['mode2.strongBranchThreshold'])
mode2Options.epsilon = float(config['Assembly']['mode2.epsilon'])
mode2Options.minConcordantReadCountForBubbleRemoval = int(config['Assembly']['mode2.bubbleRemoval.minConcordantReadCount'])
mode2Options.maxDiscordantReadCountForBubbleRemoval = int(config['Assembly']['mode2.bubbleRemoval.maxDiscordantReadCount'])
mode2Options.minLogPForBubbleRemoval = float(config['Assembly']['mode2.bubbleRemoval.minlogP'])
mode2Options.componentSizeThresholdForBubbleRemoval = int(config['Assembly']['mode2.bubbleRemoval.componentSizeThreshold'])
mode2Options.minConcordantReadCountForPhasing = int(config['Assembly']['mode2.phasing.minConcordantReadCount'])
mode2Options.maxDiscordantReadCountForPhasing = int(config['Assembly']['mode2.phasing.maxDiscordantReadCount'])
mode2Options.minLogPForPhasing = float(config['Assembly']['mode2.phasing.minlogP'])
mode2Options.maxSuperbubbleSize = int(config['Assembly']['mode2.superbubble.maxSize'])
mode2Options.maxSuperbubbleChunkSize = int(config['Assembly']['mode2.superbubble.maxChunkSize'])
mode2Options.maxSuperbubbleChunkPathCount = int(config['Assembly']['mode2.superbubble.maxChunkPathCount'])
mode2Options.superbubbleEdgeLengthThreshold = int(config['Assembly']['mode2.superbubble.edgeLengthThreshold'])
mode2Options.suppressGfaOutput = ast.literal_eval(config['Assembly']['mode2.suppressGfaOutput'])
mode2Options.suppressFastaOutput = ast.literal_eval(config['Assembly']['mode2.suppressFastaOutput'])
mode2Options.suppressDetailedOutput = ast.literal_eval(config['Assembly']['mode2.suppressDetailedOutput'])
mode2Options.suppressPhasedOutput = ast.literal_eval(config['Assembly']['mode2.suppressPhasedOutput'])
mode2Options.suppressHaploidOutput = ast.literal_eval(config['Assembly']['mode2.suppressHaploidOutput'])
a.createAssemblyGraph2(
pruneLength = int(config['Assembly']['pruneLength']),
mode2Options = mode2Options,
threadCount = 0,
debug = debug
)
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