def main(argv):
if len(argv[1:]) == 3:
input1dir = argv[1]
input2dir = argv[2]
outputdir = argv[3]
else:
print("Three arguements are needed!!")
output = open(outputdir, 'w')
try:
all_reads = open(input1dir, 'r')
except IOError:
print ("no such file!")
readslist = []
with open(input2dir, 'r') as inputfile:
f = csv.DictReader(inputfile)
for row in f:
readslist.append(row['read']) # all the reads
print("total reads in filter list:", len(readslist))
subset = Subsampling()
subset.exclude_fa(all_reads, readslist, output)
def main(argv):
start_time = time.clock()
if len(argv[1:]) == 3:
input1dir = argv[1]
input2dir = argv[2]
outputdir = argv[3]
else:
print("Three arguements are needed!!")
output = open(outputdir, 'w')
try:
all_reads = open(input1dir, 'r')
except IOError:
print ("no such file!")
readslist = []
with open(input2dir, 'r') as inputfile:
f = csv.DictReader(inputfile, delimiter =",", fieldnames=['id','reads','taxa'])
for row in f:
readslist.append(row['reads']) # all the reads
print("total reads in filter list:", len(readslist))
subset = Subsampling()
subset.exclude_fa(all_reads, readslist, output)
print time.clock() - start_time, "seconds"
