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 ('-p', '--numproc'):
num_proc = int(arg)
elif opt in ('-s', '--single'):
singleInstance = True
### use -p option for multiprocessing
num_proc = -1
###
hashobject = StreamingEigenhashes(inputdir, outputdir, get_pool=num_proc)
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]
corpus = hashobject.kmer_corpus_from_disk()
# This is a hack. Should do a better job chosing num_dims
lsi = hashobject.train_kmer_lsi(corpus,
num_dims=len(hashobject.path_dict) * 4 / 5,
single=singleInstance)
lsi.save(hashobject.output_path + 'kmer_lsi.gensim')
print help_message
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 ('-p','--numproc'):
num_proc = int(arg)
elif opt in ('-s','--single'):
singleInstance = True
### use -p option for multiprocessing
num_proc = -1
###
hashobject = StreamingEigenhashes(inputdir,outputdir,get_pool=num_proc)
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]
corpus = hashobject.kmer_corpus_from_disk()
# This is a hack. Should do a better job chosing num_dims
lsi = hashobject.train_kmer_lsi(corpus,num_dims=len(hashobject.path_dict)*4/5,single=singleInstance)
lsi.save(hashobject.output_path+'kmer_lsi.gensim')
