import glob, os
import numpy as np
from streaming_eigenhashes import StreamingEigenhashes
help_message = "usage example: python kmer_corpus.py -i /project/home/hashed_reads/ -o /project/home/cluster_vectors/"
if __name__ == "__main__":
try:
opts, args = getopt.getopt(sys.argv[1:], "hi:o:r:", ["inputdir=", "outputdir=", "filerank="])
except:
print help_message
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"):
print help_message
sys.exit()
elif opt in ("-r", "--filerank"):
fr = int(arg) - 1
elif opt in ("-i", "--inputdir"):
inputdir = arg
if inputdir[-1] != "/":
inputdir += "/"
elif opt in ("-o", "--outputdir"):
outputdir = arg
if outputdir[-1] != "/":
outputdir += "/"
hashobject = StreamingEigenhashes(inputdir, outputdir, get_pool=False)
Kmer_Hash_Count_Files = glob.glob(os.path.join(hashobject.input_path, "*.count.hash"))
# M = np.load(hashobject.input_path+'column_mask.npy')
M = []
hashobject.kmer_corpus_to_disk(Kmer_Hash_Count_Files[fr], mask=M)
dest='task_rank',
type=int,
metavar='<task_rank>',
help='The rank of the currant task.')
args = parser.parse_args()
return args
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 += '/'
task_rank = args.task_rank - 1
hashobject = StreamingEigenhashes(input_dir, output_dir, get_pool=False)
Kmer_Hash_Count_Files = glob.glob(
os.path.join(hashobject.input_path, '*.count.hash'))
# M = np.load(hashobject.input_path + 'column_mask.npy')
M = []
print("[KmerCorpus] Computing kmer corpus.")
hashobject.kmer_corpus_to_disk(Kmer_Hash_Count_Files[task_rank], mask=M)
print("[KmerCorpus] Done.")
