def cluster(self,preprocess=False): # preprocess=False by Nafiz
print "Clustering"
if preprocess:
fasta.preprocess(self.cand_context_genes_tab,
self.cand_context_genes_fasta)
self.clusterer = cdhit.CDHit(self.cand_context_genes_fasta,
self.cand_context_cluster,
self.similarity)
self.clusterer.run()
self.clusterer.parseClusters()
self.clusterer.dump(self.clusterpickle)
def cluster(self,preprocess=False,numThreads=8,mem=6000):
print "Clustering"
if preprocess:
fasta.preprocess(self.cand_context_genes_tab,
self.cand_context_genes_fasta)
self.clusterer = cdhit.CDHit(self.cand_context_genes_fasta,
self.cand_context_cluster,
self.similarity,
numThreads,mem)
self.clusterer.run()
self.clusterer.parseClusters()
self.clusterer.dump(self.clusterpickle)
