def _add_contig(self, ctg, min_length=1):
if len(ctg) < min_length:
return
assert ctg.id not in self.contigs
assert len(ctg) > 0
self.contigs[ctg.id] = contig.Contig(ctg, verbose=self.verbose)
self.contig_lengths[ctg.id] = [[len(self.contigs[ctg.id]), 0, 0]]
def test_extend(self):
'''Test extend'''
ctg = contig.Contig(sequences.Fasta('ID', 'ACCGT'))
self.assertEqual(ctg.extend(5, 2, 100), (0, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'ACCGT'))
ctg.add_left_kmer('GT')
self.assertEqual(ctg.extend(1, 2, 100), (2, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGT'))
self.assertEqual(ctg.extend(1, 2, 100), (0, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGT'))
ctg.add_right_kmer('TG')
self.assertEqual(ctg.extend(1, 2, 100), (0, 2))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGTTG'))
self.assertEqual(ctg.extend(1, 2, 100), (0, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGTTG'))
ctg.add_left_kmer('AG')
ctg.add_right_kmer('GC')
self.assertEqual(ctg.extend(1, 2, 100), (2, 2))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'AGGTACCGTTGGC'))
def test_len(self):
'''Test len'''
ctg = contig.Contig(sequences.Fasta('ID', 'ACCGT'))
self.assertEqual(len(ctg), 5)
def test_add_right_kmer(self):
'''Test add_right_kmer'''
ctg = contig.Contig(sequences.Fasta('ID', 'ACCGT'))
ctg.add_right_kmer('GT')
self.assertListEqual(ctg.right_kmers.kmers, ['GT'])
def test_init(self):
'''Test init'''
ctg = contig.Contig(sequences.Fasta('ID', 'ACCGT'))
self.assertTrue(ctg.fa, sequences.Fasta('ID', 'ACCGT'))