inputdir = arg
if inputdir[-1] != '/':
inputdir += '/'
elif opt in ('-o', '--outputdir'):
outputdir = arg
if outputdir[-1] != '/':
outputdir += '/'
elif opt in ('-r', '--filerank'):
fr = int(arg) - 1
elif opt in ('-t', '--thresh'):
thresh = float(arg)
hashobject = StreamingEigenhashes(inputdir, outputdir, get_pool=-1)
Kmer_Hash_Count_Files = glob.glob(
os.path.join(hashobject.input_path, '*.count.hash.conditioned'))
hashobject.path_dict = {}
for i in range(len(Kmer_Hash_Count_Files)):
hashobject.path_dict[i] = Kmer_Hash_Count_Files[i]
lsi = models.LsiModel.load(hashobject.output_path + 'kmer_lsi.gensim')
Index = np.load(hashobject.output_path + 'cluster_index.npy')
i = fr * 10**6
o = (i, min(10**6, 2**hashobject.hash_size - i))
hashobject.cluster_thresh = thresh
Ci = hashobject.lsi_cluster_part(o, lsi, Index)
for ci, c in enumerate(Ci):
try:
np.save(hashobject.output_path + str(ci) + '/' + str(fr) + '.npy',
c)
except IOError:
os.system('mkdir ' + hashobject.output_path + str(ci))
np.save(hashobject.output_path + str(ci) + '/' + str(fr) + '.npy',
c)
print help_message
sys.exit()
elif opt in ('-i','--inputdir'):
inputdir = arg
if inputdir[-1] != '/':
inputdir += '/'
elif opt in ('-o','--outputdir'):
outputdir = arg
if outputdir[-1] != '/':
outputdir += '/'
elif opt in ('-r','--filerank'):
fr = int(arg) - 1
elif opt in ('-t','--thresh'):
thresh = float(arg)
hashobject = StreamingEigenhashes(inputdir,outputdir,get_pool=-1)
Kmer_Hash_Count_Files = glob.glob(os.path.join(hashobject.input_path,'*.count.hash.conditioned'))
hashobject.path_dict = {}
for i in range(len(Kmer_Hash_Count_Files)):
hashobject.path_dict[i] = Kmer_Hash_Count_Files[i]
lsi = models.LsiModel.load(hashobject.output_path+'kmer_lsi.gensim')
Index = np.load(hashobject.output_path+'cluster_index.npy')
i = fr*10**6
o = (i,min(10**6,2**hashobject.hash_size-i))
hashobject.cluster_thresh = thresh
Ci = hashobject.lsi_cluster_part(o,lsi,Index)
for ci,c in enumerate(Ci):
try:
np.save(hashobject.output_path+str(ci)+'/'+str(fr)+'.npy',c)
except IOError:
os.system('mkdir '+hashobject.output_path+str(ci))
np.save(hashobject.output_path+str(ci)+'/'+str(fr)+'.npy',c)
