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)