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import unittest
import sys
import os
from collections import Counter
import dna_jellyfish as jf
class TestMerFile(unittest.TestCase):
def setUp(self):
self.mf = jf.ReadMerFile(os.path.join(data, "swig_python.jf"))
def test_histo(self):
histo = Counter()
while self.mf.next_mer():
histo[self.mf.count()] += 1
jf_histo = Counter()
with open(os.path.join(data, "swig_python.histo")) as f:
for line in f:
num, count = [int(n) for n in line.split()]
self.assertEqual(count, histo[num])
def test_dump(self):
good = True
with open(os.path.join(data, "swig_python.dump")) as f:
for line in f:
good = good and self.mf.next_mer()
if not good: break
a = line.split()
good = good and a[0] == str(self.mf.mer()) and int(a[1]) == self.mf.count()
if not good: break
self.assertTrue(good)
def test_iter(self):
good = True
with open(os.path.join(data, "swig_python.dump")) as f:
for mer, count in self.mf:
line = f.readline()
good = good and line
if not good: break
fmer, fcount = line.split()
good = good and fmer == str(mer) and int(fcount) == count
if not good: break
self.assertTrue(good)
line = f.readline()
self.assertTrue(not line)
def test_query(self):
good = True
qf = jf.QueryMerFile(os.path.join(data, "swig_python.jf"))
for mer, count in self.mf:
good = good and count == qf[mer]
if not good: break
self.assertTrue(good)
if __name__ == '__main__':
data = sys.argv.pop(1)
unittest.main()
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