writer_vir.writerow(['partition'] + ['alignment','alignment length']*10)
f_counts = open(inputdir+'partition_read_counts_by_sample.csv','w')
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:
