def test_vcf_to_seqs_indels1(self):
input = ['thecontig', '5', '.', 'AT', 'A', '.', '.', '.', 'GT:AD', '0/1:2,10']
actual = assembly.vcf_to_seqs([input], {'thecontig': 10}, ['s1'], min_dp=2)
actual = list(actual)[0][1].strip('N')
self.assertEqual(actual, 'A')
actual = assembly.vcf_to_seqs([input], {'thecontig': 10}, ['s1'], min_dp=2)
actual = list(actual)[0][1]
self.assertEqual(actual, 'NNNNANNNN')
def test_vcf_to_seqs_indels1(self):
input = ['thecontig', '5', '.', 'AT', 'A', '.', '.', '.', 'GT:AD', '0/1:2,10']
actual = assembly.vcf_to_seqs([input], {'thecontig': 10}, ['s1'], min_dp=2)
actual = list(actual)[0][1].strip('N')
self.assertEqual(actual, 'A')
actual = assembly.vcf_to_seqs([input], {'thecontig': 10}, ['s1'], min_dp=2)
actual = list(actual)[0][1]
self.assertEqual(actual, 'NNNNANNNN')
def test_vcf_to_seqs_indels2(self):
''' More end-to-end indel handling '''
myInputDir = util.file.get_test_input_path(self)
input = os.path.join(myInputDir, 'indel.vcf.gz')
expected = os.path.join(myInputDir, 'output.fasta')
chrlens = {'EBOV_2014_G6060.1': 18962}
samples = ['G6060.1']
expected = str(Bio.SeqIO.read(expected, 'fasta').seq)
actual = assembly.vcf_to_seqs(util.file.read_tabfile(input), chrlens, samples, min_dp=2)
actual = list(actual)[0][1].strip('N')
self.assertEqual(actual, expected)
def test_vcf_to_seqs_indels2(self):
''' More end-to-end indel handling '''
myInputDir = util.file.get_test_input_path(self)
input = os.path.join(myInputDir, 'indel.vcf.gz')
expected = os.path.join(myInputDir, 'output.fasta')
chrlens = {'EBOV_2014_G6060.1': 18962}
samples = ['G6060.1']
expected = str(Bio.SeqIO.read(expected, 'fasta').seq)
actual = assembly.vcf_to_seqs(util.file.read_tabfile(input), chrlens, samples, min_dp=2)
actual = list(actual)[0][1].strip('N')
self.assertEqual(actual, expected)