try:
opts, args = getopt.getopt(
sys.argv[1:], 'hi:o:k:s:',
["inputdir=", "outputdir=", "kmersize=", "hashsize="])
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 += '/'
elif opt in ('-k', '--kmersize'):
k_size = int(arg)
elif opt in ('-s', '--hashsize'):
h_size = int(arg)
hashobject = Fastq_Reader(inputdir, outputdir, new_hash=(h_size, k_size))
total_rand_kmers = k_size * h_size * 2
hashobject.rand_kmers_for_wheel(total_rand_kmers)
hashobject.set_wheels(wheels=1)
os.system('rm %s/random_kmers.fastq' % inputdir)
f = open(outputdir + 'hashParts.txt', 'w')
f.write('%d\n' % (2**h_size / 10**6 + 1))
f.close()
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())
help_message = 'usage example: python assembly_summary.py -i /project/home/'
if __name__ == "__main__":
try:
opts, args = getopt.getopt(sys.argv[1:],'hi:',["inputdir="])
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 += '/'
hashobject = Fastq_Reader(inputdir+'read_partitions/',inputdir+'read_partitions/')
f = open(bact_names_path)
BNames = cPickle.load(f)
f.close()
f = open(vir_names_path)
VNames = cPickle.load(f)
f.close()
f = open(inputdir+'lib_estimates/samples_grouped_by_lib.csv')
reader = csv.reader(f)
Sample_ids = []
for row in reader:
Sample_ids += row
f.close()
f_main = open(inputdir+'assembly_alignment_summary.csv','w')
writer_main = csv.writer(f_main)
writer_main.writerow(['partition','N50','largest contig','total bp','scaffolds','top bacterial alignment','alignment length','top viral alignment','alignment length'])
