def test_invert_match_generator_bad_pos1(self):
pos_text = self.pos_text[:]
pos_text.insert(0, "3.5 bad position")
pos_txt = StringIO(''.join(pos_text))
vcf_txt = StringIO(''.join(self.vcf_text))
with self.assertRaises(ValueError):
_ = list(grep_vcf.invert_match_generator(pos_txt, vcf_txt))
def test_invert_match_trunked_pos(self):
# pos < vcf and pos file is shorter than vcf file
pos_txt = StringIO('7\tline 1\n')
vcf_txt = StringIO('9\tvcf 1\n10\tvcf 2\n11\tvcf 3\n')
diff = list(grep_vcf.invert_match_generator(pos_txt, vcf_txt))
self.assertListEqual(diff,
['9\tvcf 1\n', '10\tvcf 2\n', '11\tvcf 3\n'])
def test_invert_match_generator_bad_vcf3(self):
pos_txt = StringIO(''.join(self.pos_text))
vcf_text = self.vcf_text[:]
vcf_text.insert(3, "8.5\tbad position\n")
vcf_txt = StringIO(''.join(vcf_text))
with self.assertRaises(ValueError):
_ = list(grep_vcf.invert_match_generator(pos_txt, vcf_txt))
def test_invert_match_generator(self):
pos_txt = StringIO(''.join(self.pos_text))
vcf_txt = StringIO(''.join(self.vcf_text))
diff = list(grep_vcf.invert_match_generator(pos_txt, vcf_txt))
self.assertListEqual(diff, [
"7\tvcf line 1\n",
"12\tvcf line 5\n",
])
def test_invert_match_trunked_vcf2(self):
# vcf < pos and vcf file is shorter than pos file
pos_txt = StringIO('9\tline 1\n10\tline 2\n')
vcf_txt = StringIO('8\tvcf 1\n')
diff = list(grep_vcf.invert_match_generator(pos_txt, vcf_txt))
self.assertListEqual(diff, ['8\tvcf 1\n'])
def test_invert_match_empty_vcf(self):
pos_txt = StringIO(''.join(self.pos_text[:]))
vcf_txt = StringIO('')
diff = list(grep_vcf.invert_match_generator(pos_txt, vcf_txt))
self.assertListEqual(diff, [])
def test_invert_match_empty_pos(self):
pos_txt = StringIO('')
vcf_txt = StringIO(''.join(self.vcf_text))
diff = list(grep_vcf.invert_match_generator(pos_txt, vcf_txt))
expected_lines = [l for l in self.vcf_text if l[0] not in ('#', '\n')]
self.assertListEqual(diff, expected_lines)