try:
sample_counts.append(sum(hashobject.read_counts(c+'.'+sample).values()))
except:
sample_counts.append(0)
writer_main.writerow([c[:c.index('.cluster')],asbly.get('N50',0),asbly.get('largest contig',0),asbly.get('total bp',0),asbly.get('num scaffolds',0),BNames.get(algn[0][0],''),algn[0][1],VNames.get(algn_v[0][0],''),algn_v[0][1]])
brow = [c[:c.index('.cluster')]]
for a in algn[:10]:
brow += [BNames.get(a[0],''),a[1]]
writer_bact.writerow(brow)
vrow = [c[:c.index('.cluster')]]
for a in algn_v[:10]:
vrow += [VNames.get(a[0],''),a[1]]
writer_vir.writerow(vrow)
writer_counts.writerow([c[:c.index('.cluster')]] + sample_counts)
try:
A = hashobject.phyler_stats(c,level='genus')
PGenus[c] = {}
for a in A:
Genus[a[0]] += a[2]
PGenus[c][a[0]] = a[1]
except:
PGenus[c] = {}
try:
A = hashobject.phyler_stats(c,level='family')
PFamily[c] = {}
for a in A:
Family[a[0]] += a[2]
PFamily[c][a[0]] = a[1]
except:
PFamily[c] = {}
Genus = sorted(Genus.items(),key=itemgetter(1),reverse=True)
