import numpy as np
from streaming_eigenhashes import StreamingEigenhashes
help_message = 'usage example: python kmer_clusters.py -i /project/home/hashed_reads/ -o /project/home/cluster_vectors/'
if __name__ == "__main__":
try:
opts, args = getopt.getopt(sys.argv[1:], 'hi:o:',
["inputdir=", "outputdir="])
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 ('-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, '*.nonzero.npy'))
corpus_generator = hashobject.corpus_idf_from_hash_paths(
Kmer_Hash_Count_Files)
hashobject.train_tfidf(corpus_generator)
np.save(hashobject.output_path + 'global_weights.npy',
hashobject.global_weights)
import sys, getopt
import glob, os
from gensim import corpora
import numpy as np
from streaming_eigenhashes import StreamingEigenhashes
help_message = 'usage example: python kmer_clusters.py -i /project/home/hashed_reads/ -o /project/home/cluster_vectors/'
if __name__ == "__main__":
try:
opts, args = getopt.getopt(sys.argv[1:],'hi:o:',["inputdir=","outputdir="])
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 ('-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,'*.nonzero.npy'))
corpus_generator = hashobject.corpus_idf_from_hash_paths(Kmer_Hash_Count_Files)
hashobject.train_tfidf(corpus_generator)
np.save(hashobject.output_path+'global_weights.npy',hashobject.global_weights)
