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#!/usr/bin/python3
import shasta
import GetConfig
import ast
import sys
# Read the config file.
config = GetConfig.getConfig()
# Initialize the assembler and access what we need.
a = shasta.Assembler()
a.accessKmers()
a.accessMarkers()
a.accessAlignmentData()
a.accessReadGraph()
# Create vertices of the marker graph.
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()
# Create edges of the marker graph.
a.createMarkerGraphEdges()
a.findMarkerGraphReverseComplementEdges()
# Approximate transitive reduction.
a.transitiveReduction(
lowCoverageThreshold = int(config['MarkerGraph']['lowCoverageThreshold']),
highCoverageThreshold = int(config['MarkerGraph']['highCoverageThreshold']),
maxDistance = int(config['MarkerGraph']['maxDistance']),
edgeMarkerSkipThreshold = int(config['MarkerGraph']['edgeMarkerSkipThreshold']),
)
# Prune the strong subgraph of the marker graph.
a.pruneMarkerGraphStrongSubgraph(
iterationCount = int(config['MarkerGraph']['pruneIterationCount']))
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