writer_counts = csv.writer(f_counts) writer_counts.writerow(['partition']+Sample_ids) f_genus = open(inputdir+'partition_abundance_genus.csv','w') writer_genus = csv.writer(f_genus) Genus = defaultdict(int) PGenus = {} f_family = open(inputdir+'partition_abundance_family.csv','w') writer_family = csv.writer(f_family) Family = defaultdict(int) PFamily = {} FP = glob.glob(os.path.join(inputdir+'cluster_vectors/','*.cluster.npy')) Clusters = [fp[fp.rfind('/')+1:fp.index('.npy')] for fp in FP] for c in Clusters: hashobject.assembly_loc = hashobject.output_path+c+'_velvet/' try: asbly = hashobject.assembly_stats(c) except: asbly = {} try: algn = hashobject.alignment_stats(c) algn = sorted(algn.iteritems(),key=itemgetter(1),reverse=True) if len(algn) == 0: algn = [(None,0)] except: algn = [(None,0)] try: algn_v = hashobject.alignment_stats(c+'.viral') algn_v = sorted(algn_v.iteritems(),key=itemgetter(1),reverse=True) if len(algn_v) == 0: algn_v = [(None,0)] except: