Commit cfb160ee by Eric Coissac

Remove non useful import and add logger to the scaffold call

parent 0d8a1586
......@@ -4,14 +4,10 @@ Created on 28 sept. 2014
@author: coissac
'''
import orgasm.samples
from orgasm import getIndex, getSeeds,getOutput
from orgasm.tango import cutLowCoverage, cutSNPs,\
estimateDeadBrancheLength, estimateFragmentLength,\
genesincontig, scaffold, fillGaps, dumpGraph, restoreGraph
import sys
from orgasm.tango import estimateFragmentLength,\
genesincontig, scaffold, restoreGraph
__title__="Recompact the assembling graph"
......@@ -66,7 +62,8 @@ def run(config):
cg = asm.compactAssembling(verbose=False)
logger.info("Scaffold the assembly")
scaffold(asm,cg,minlink=5,back=int(back),addConnectedLink=False)
scaffold(asm,cg,minlink=5,back=int(back),addConnectedLink=False,
logger=logger)
genesincontig(cg,r,x)
with open(output+'.gml','w') as gmlfile:
print(cg.gml(),file=gmlfile)
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