return args
# MAIN
if __name__ == "__main__":
args = interface()
input_dir = os.path.abspath(args.IN)
if not input_dir.endswith('/'):
input_dir += '/'
output_dir = os.path.abspath(args.OUT)
if not output_dir.endswith('/'):
output_dir += '/'
thresh = args.threshold
hashobject = StreamingEigenhashes(input_dir, output_dir, 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')
hashobject.cluster_thresh = thresh
Index = hashobject.lsi_cluster_index(lsi)
np.save(hashobject.output_path + 'cluster_index.npy', Index)
print('Cluster index has shape: ' + str(Index.shape))
with open(hashobject.output_path + 'numClusters.txt', 'w') as f:
f.write('{0}\n'.format(Index.shape[0]))
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"):
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")
hashobject.cluster_thresh = thresh
Index = hashobject.lsi_cluster_index(lsi)
np.save(hashobject.output_path + "cluster_index.npy", Index)
print "cluster index has shape:", Index.shape
f = open(hashobject.output_path + "numClusters.txt", "w")
f.write("%d\n" % Index.shape[0])
f.close()
