def test_create_vcf_from_sequences(self, temp_mock, ctx_tempfile_mock,
ctx_tempdir_mock):
builder = SNPFeatureBuilder()
temp_vcf_file = tempfile.NamedTemporaryFile('w', delete=False)
temp_files = []
temp_folders = []
ctx_tempfile_mock.side_effect = create_context_aware_tempfile_mock(temp_files)
ctx_tempdir_mock.side_effect = create_context_aware_tempdir_mock(temp_folders)
temp_mock.NamedTemporaryFile.return_value = temp_vcf_file
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
fasta_file = open(fasta_filename, 'r')
builder.load_fasta_sequences(fasta_file)
builder.create_vcf_from_sequences()
self.assertEqual(len(temp_files), 1)
self.assertFalse(os.path.isfile(temp_files[0]))
self.assertEqual(len(temp_folders), 1)
self.assertFalse(os.path.isdir(temp_folders[0]))
self.assertTrue(os.path.isfile(temp_vcf_file.name))
builder.vcf_input_file.seek(0)
records = SNPSitesReader(builder.vcf_input_file)
number_of_records = sum((1 for record in records))
self.assertEqual(number_of_records, 5)
fasta_file.close()
temp_vcf_file.close()
os.remove(temp_vcf_file.name)
def test_next_with_GT(self):
"""Parse a file which already in Genotype format"""
vcf_filename = os.path.join(test_data(), 'file_with_SNPs_in_GT_format.aln.vcf')
vcf_file = open(vcf_filename, 'r')
reader = SNPSitesReader(vcf_file)
record = reader.next()
samples = record.samples
samples_with_alternative_bases = [sample.sample for sample in samples if
sample.data.GT != '0']
expected = ['3002_8_1', '3002_8_2', '3002_8_6', '4056_2_10', '4056_2_4',
'4056_8_6', '5174_5_1', '5174_5_7', '5174_5_9', '5174_6_10',
'5174_7_1', '5174_8_5']
self.assertItemsEqual(samples_with_alternative_bases, expected)
def test_next(self):
"""Parse a file with Alternate Base info
File was cerated using snp-sites"""
vcf_filename = os.path.join(test_data(), 'file_with_SNPs.aln.vcf')
vcf_file = open(vcf_filename, 'r')
reader = SNPSitesReader(vcf_file)
record = reader.next()
samples = record.samples
samples_with_alternative_bases = [sample.sample for sample in samples if
sample.data.GT != '0']
expected = ['3002_8_1', '3002_8_2', '3002_8_6', '4056_2_10', '4056_2_4',
'4056_8_6', '5174_5_1', '5174_5_7', '5174_5_9', '5174_6_10',
'5174_7_1', '5174_8_5']
self.assertItemsEqual(samples_with_alternative_bases, expected)
def test_ammend_line(self):
snp_sites_old_bases = SNPSitesReader.__bases__
SNPSitesReader.__bases__ = (MagicMock,) # I don't want to test vcf.Reader
reader = SNPSitesReader()
reader._separator="\t| +"
line = "0\t1\t2\tC\tT,G\t5\t6\tAB\t.\tG\t.\tT"
expected = "0\t1\t2\tC\tT,G\t5\t6\t.\tGT\t2\t0\t1"
self.assertEqual(reader._amend_line(line), expected)
# It would be elegant if it maintained the separator but this is unlikely to
# case big issues, hopefully
line = "0 1 2 C T,G 5 6 AB . G . T"
expected = "0\t1\t2\tC\tT,G\t5\t6\t.\tGT\t2\t0\t1"
self.assertEqual(reader._amend_line(line), expected)
line = "0 1 2 C T,G\t5\t6 AB . G . T"
expected = "0\t1\t2\tC\tT,G\t5\t6\t.\tGT\t2\t0\t1"
self.assertEqual(reader._amend_line(line), expected)
line = "0\t1\t2\tC\tT,G\t5\t6\tAB\tGT\t2\t0\t1"
expected = "0\t1\t2\tC\tT,G\t5\t6\tAB\tGT\t2\t0\t1"
self.assertEqual(reader._amend_line(line), expected)
SNPSitesReader.__bases__ = snp_sites_old_bases
str(new_amino_acid))
consequence = Consequence(alternative_base,
Consequence=consequence_type,
Protein_position=position_in_protein,
Amino_acids=amino_acid_change,
STRAND=strand)
consequences.append(consequence)
return consequences
if __name__ == '__main__':
args = get_arguments()
vcf_input_file, gff_input_file, fasta_input_file, vcf_output_file = get_file_handles(
args)
vcf_input_reader = SNPSitesReader(vcf_input_file)
add_consequences_info_header(vcf_input_reader)
add_GT_format_header(vcf_input_reader)
remove_AB_info_header(vcf_input_reader)
vcf_output_writer = vcf.Writer(vcf_output_file, vcf_input_reader)
sequence = Bio.SeqIO.parse(fasta_input_file, 'fasta').next()
feature_index = build_feature_index(gff_input_file)
chromosome_name_in_vcf = '1'
chromosome_name_in_gff = 'Salmonella_enterica_subsp_enterica_serovar_Typhi_str_CT18_v1|SC|contig000001'
for record in vcf_input_reader:
if record.CHROM == chromosome_name_in_vcf:
matching_cds = get_matching_CDS(record, feature_index,
chromosome_name_in_gff)
