Commit 80be8f89 by Eric Coissac

Change unfold command according to the new unfold algorithm

parent 9b9eef59
......@@ -75,7 +75,7 @@ def run(config):
r = getIndex(config)
coverage,x,newprobes = getSeeds(r,config)
coverage,x,newprobes = getSeeds(r,config) # @UnusedVariable
asm = restoreGraph(output+'.oax',r,x)
......@@ -102,11 +102,11 @@ def run(config):
genesincontig(cg,r,x)
minlink=config['orgasm']['minlink']
constraints = pathConstraints(asm,cg,back=int(back),minlink=minlink)
scaffold(asm,cg,minlink=minlink,
back=int(back),addConnectedLink=False,
logger=logger)
constraints = pathConstraints(asm,cg,back=int(back),minlink=minlink)
#fastaout = open(output+".fasta","w")
fastaout = sys.stdout
......@@ -132,10 +132,13 @@ def run(config):
seeds=seeds,
constraints=constraints,
circular=config['unfold']['circular'],
force=config['unfold']['force'])
force=config['unfold']['force'],
logger=logger)
path = path[-1][0]
logger.info("Expanded path : %s" % str(path))
if config['unfold']['format']=="fasta":
fa = path2fasta(asm,cg,path,
identifier="%s_%d" % (seqid,c),
......
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