def main():
if not len(sys.argv) in [3]:
print 'Usage: '
print ' %s data index' % sys.argv[0]
os.abort()
else:
if not isfile(sys.argv[1]):
print "Input file doesn't exist"
os.abort()
inp = open(sys.argv[1])
# read input
data = inp.read()
# create index
idx = fmindex.index(data)
# save index to file
fmindex.save(sys.argv[2], idx)
print "search results: "
list_matches = idx.search(
"ctaactgataccggaataccttaactacggacgtttgtttttgcgccacgc")
for each in list_matches:
print each
def main():
if not len(sys.argv) in [3]:
print('Usage: ')
print(' %s data index' % sys.argv[0])
os.abort()
else:
if not isfile(sys.argv[1]):
print("Input file doesn't exist")
os.abort()
inp = open(sys.argv[1])
data = inp.read()
idx = fmindex.index(data)
fmindex.save(sys.argv[2], idx)
def main():
if not len(sys.argv) in [3]:
print 'Usage: '
print ' %s data index' % sys.argv[0]
os.abort()
else:
if not isfile(sys.argv[1]):
print "Input file doesn't exist"
os.abort()
inp = open(sys.argv[1])
# read input
data = inp.read()
# create index
idx = fmindex.index(data)
# save index to file
fmindex.save(sys.argv[2], idx)
def main():
if not len(sys.argv) in [3]:
print 'Usage: '
print ' %s data index' % sys.argv[0]
os.abort()
else:
if not isfile(sys.argv[1]):
print "Input file doesn't exist"
os.abort()
inp = open(sys.argv[1])
# read input
data = inp.read()
# create index
idx = fmindex.index(data)
# save index to file
fmindex.save(sys.argv[2], idx)
def main():
tim = time.clock
index = []
# Run the above function and store its results in a variable.
full_file_paths = get_filepaths(sys.argv[1])
#print(full_file_paths)
t_start = tim()
for f in full_file_paths:
print(f)
inp = open(f)
# read input
data = inp.read()
s = data.split('\n', 1)[-1].replace("\n", "")
#print(concat_rc(s))
index.append(fmindex.index(concat_rc(s)))
t_load = tim()
print("Number of genomes: " + str(len(index)))
print("Indexing: %sms" % diff_time(t_start, t_load))
time.sleep(5)
lines2 = [line.rstrip('\n') for line in open(sys.argv[2])]
lines3 = [line.rstrip('\n') for line in open(sys.argv[3])]
#print(lines2)
idx2 = []
idx3 = []
read2 = []
read3 = []
for i in range(len(lines2)):
if i%4 == 0:
idx2.append(lines2[i])
idx3.append(lines3[i])
for i in range(len(lines3)):
if i%4 == 1:
read2.append(lines2[i])
read3.append(lines3[i])
#print(idx2)
#print(read2)
for r in range(len(read2)):
print(read2[r])
print(idx2[r])
tmp1 = tim()
for i in range(len(index)):
if index[i].search(read2[r]):
#print(index[i].search(r))
print(full_file_paths[i])
time.sleep(0.5)
break
tmp2 = tim()
print("Search: %sms" % diff_time(tmp1, tmp2))
for r in range(len(read3)):
print(read3[r])
print(idx3[r])
tmp1 = tim()
for i in range(len(index)):
if index[i].search(read3[r]):
#print(index[i].search(r))
print(full_file_paths[i])
time.sleep(0.5)
break
tmp2 = tim()
print("Search: %sms" % diff_time(tmp1, tmp2))
