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import unittest
import sys
import random
import dna_jellyfish as jf
class TestStringMers(unittest.TestCase):
def setUp(self):
bases = "ACGTacgt"
self.str = ''.join(random.choice(bases) for _ in range(1000))
self.k = random.randint(10, 110)
jf.MerDNA.k(self.k)
def test_all_mers(self):
count = 0
good1 = True
good2 = True
mers = jf.string_mers(self.str)
for m in mers:
m2 = jf.MerDNA(self.str[count:count+self.k])
good1 = good1 and m == m2
good2 = good2 and self.str[count:count+self.k].upper() == str(m2)
count += 1
self.assertTrue(good1)
self.assertTrue(good2)
self.assertEqual(len(self.str) - self.k + 1, count)
def test_canonical_mers(self):
good = True
mers = jf.string_canonicals(self.str)
for count, m in enumerate(mers):
m2 = jf.MerDNA(self.str[count:count+self.k])
rm2 = m2.get_reverse_complement()
good = good and (m == m2 or m == rm2)
good = good and (not (m > m2)) and (not (m > rm2))
# count += 1
self.assertTrue(good)
self.assertEqual(len(self.str) - self.k + 0, count)
if __name__ == '__main__':
data = sys.argv.pop(1)
unittest.main()
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