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#!/usr/bin/python3
import shasta
import argparse
# Parse the arguments.
parser = argparse.ArgumentParser(description=
'Assembly graph detangling using path following.')
parser.add_argument('stage', type=str)
parser.add_argument('component', type=int)
arguments = parser.parse_args()
stage = arguments.stage
component = arguments.component
# Get Shasta options.
options = shasta.AssemblerOptions('shasta.conf')
# Create the Assembler and access what we need.
assembler = shasta.Assembler()
assembler.accessMarkers()
assembler.accessMode3Assembler()
# Create the mode3::AssemblyGraph for this assembly stage and component.
assemblyGraph = shasta.Mode3AssemblyGraph(stage, component, assembler, options.assemblyOptions.mode3Options)
# Detangle with path following.
assemblyGraph.detangle2()
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