help_message = 'usage example: python merge_hashq_files.py -r 3 -i /project/home/hashed_reads/ -o /project/home/hashed_reads/'
if __name__ == "__main__":
try:
opts, args = getopt.getopt(sys.argv[1:], 'hr:i:o:',
["filerank=", "inputdir=", "outputdir="])
except:
print help_message
sys.exit(2)
for opt, arg in opts:
if 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 += '/'
FP = glob.glob(os.path.join(inputdir, '*hashq*'))
FP = [fp[fp.rfind('/') + 1:] for fp in FP]
FP = list(set([fp[:fp.index('.')] for fp in FP]))
file_prefix = FP[fr]
hashobject = Fastq_Reader(inputdir, outputdir)
H = hashobject.merge_count_fractions(file_prefix)
H = np.array(H, dtype=np.uint16)
nz = np.nonzero(H)[0]
np.save(hashobject.output_path + file_prefix + '.nonzero.npy', nz)
print 'sample %s has %d nonzero elements and %d total observed kmers' % (
file_prefix, len(nz), H.sum())
import numpy as np
from fastq_reader import Fastq_Reader
help_message = 'usage example: python merge_hashq_files.py -r 3 -i /project/home/hashed_reads/ -o /project/home/hashed_reads/'
if __name__ == "__main__":
try:
opts, args = getopt.getopt(sys.argv[1:],'hr:i:o:',["filerank=","inputdir=","outputdir="])
except:
print help_message
sys.exit(2)
for opt, arg in opts:
if 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 += '/'
FP = glob.glob(os.path.join(inputdir,'*.hashq.*'))
FP = [fp[fp.rfind('/')+1:] for fp in FP]
FP = list(set([fp[:fp.index('.')] for fp in FP]))
file_prefix = FP[fr]
hashobject = Fastq_Reader(inputdir,outputdir)
H = hashobject.merge_count_fractions(file_prefix)
H = np.array(H,dtype=np.uint16)
nz = np.nonzero(H)[0]
np.save(hashobject.output_path+file_prefix+'.nonzero.npy',nz)
print 'sample %s has %d nonzero elements and %d total observed kmers' % (file_prefix,len(nz),H.sum())
