def test_full_coverage(self):
g = Gene('rep5.1_rep(pMW2)_NC005011', 10, 0)
self.assertTrue(g.is_full_coverage())
self.assertEqual(str(
g),
'rep5.1 Full 100 NC005011 plasmidfinder'
' rep5.1_rep(pMW2)_NC005011')
def full_gene_coverage(self, counter):
self.logger.info("Check the coverage of a sequence")
alleles = []
for (gene_name, kmers_dict) in self.fasta_obj.sequences_to_kmers.items():
kv = kmers_dict.values()
kv_total_length = len(kmers_dict)
kz = len([x for x in kv if x == 0])
kl = kv_total_length - kz
if kl > kz:
alleles.append(Gene(gene_name, kl, kz))
self.print_out_alleles(self.filter_contained_alleles(alleles))
self.identify_alleles_with_100_percent(alleles)
return alleles
def test_inc_double_dash_name(self):
g = Gene('IncFII(S).1__CP000851', 5, 5)
self.assertEqual(g.short_name(), "IncFII(S).1")
self.assertEqual(g.accession(), "CP000851")
def test_rep_with_slash_name(self):
g = Gene('rep6.1_repA(p703/5)_AF109375', 5, 5)
self.assertEqual(g.short_name(), "rep6.1")
self.assertEqual(g.accession(), "AF109375")
def test_rep_name(self):
g = Gene('rep5.1_rep(pMW2)_NC005011', 5, 5)
self.assertEqual(g.short_name(), "rep5.1")
self.assertEqual(g.accession(), "NC005011")
def test_nc_name(self):
g = Gene('Col(BS512).1__NC_010656.2', 5, 5)
self.assertEqual(g.accession(), "NC_010656.2")
self.assertEqual(g.short_name(), "Col(BS512).1")
def test_medium_coverage(self):
g = Gene('rep5.1_rep(pMW2)_NC005011', 5, 5)
self.assertFalse(g.is_full_coverage())
self.assertEqual(str(
g), 'rep5.1 Partial 50 NC005011 plasmidfinder'
' rep5.1_rep(pMW2)_NC005011')
def test_no_coverage(self):
g = Gene('rep5.1_rep(pMW2)_NC005011', 0, 10)
self.assertFalse(g.is_full_coverage())
self.assertEqual(str(g), 'rep5.1 Partial 0 NC005011 plasmidfinder rep5.1_rep(pMW2)_NC005011')