def test_vcf_reader_to_df(get_created_vcf_tabix_files):
"""Get all variants from parsed file into dataframe.
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
vcf_reader = VCFReader(vcf=vcf_file_path, bams=[], is_fp=False)
df = vcf_reader.dataframe
assert(len(vcf_reader) == len(df))
def test_vcf_loader_snps(get_created_vcf_tabix_files):
"""Get all variants from mocked file stream, filter SNPs, multi allele & multi samples
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
vcf_bam_tuple = VCFReader.VcfBamPath(vcf=vcf_file_path, bam=tabix_file_path, is_fp=False)
vcf_loader = VCFReader([vcf_bam_tuple])
assert(len(vcf_loader) == 13)
def test_vcf_load_variant_from_multiple_files(get_created_vcf_tabix_files):
"""Get variants from multiple mocked VCF files.
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
vcf_reader = VCFReader(vcf=vcf_file_path, bams=[], is_fp=False)
vcf_reader_2x = VCFReader(vcf=vcf_file_path, bams=[], is_fp=False)
assert (len(vcf_reader) == len(vcf_reader_2x))
def test_vcf_load_fp(get_created_vcf_tabix_files):
"""Get first variant from false positive mocked VCF file stream and check zygosity.
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
vcf_bam_tuple = VCFReader.VcfBamPath(vcf=vcf_file_path, bam=tabix_file_path, is_fp=True)
vcf_loader = VCFReader([vcf_bam_tuple])
for v in vcf_loader:
assert(v.zygosity == VariantZygosity.NO_VARIANT)
def test_vcf_load_fp(get_created_vcf_tabix_files):
"""Get first variant from false positive mocked VCF file stream and check zygosity.
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
vcf_reader = VCFReader(vcf=vcf_file_path, bams=[], is_fp=True, format_keys=["GT"])
for v in vcf_reader:
for i in range(len(v.samples)):
assert(v.zygosity[i] == VariantZygosity.NO_VARIANT)
def test_vcf_load_variant_from_multiple_files(get_created_vcf_tabix_files):
"""Get variants from multiple mocked VCF files.
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
first_vcf_bam_tuple = VCFReader.VcfBamPath(vcf=vcf_file_path, bam=tabix_file_path, is_fp=False)
second_vcf_bam_tuple = VCFReader.VcfBamPath(vcf=vcf_file_path, bam=tabix_file_path, is_fp=False)
vcf_loader = VCFReader([first_vcf_bam_tuple])
vcf_loader_2x = VCFReader([first_vcf_bam_tuple, second_vcf_bam_tuple])
assert (2 * len(vcf_loader) == len(vcf_loader_2x))
def test_vcf_fetch_variant(get_created_vcf_tabix_files):
"""Get first variant from mocked VCF file stream.
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
vcf_reader = VCFReader(vcf=vcf_file_path, bams=[], is_fp=False)
try:
assert (type(vcf_reader[0]) == Variant)
except IndexError:
pytest.fail("Can not retrieve first element from VCFReader")
def test_vcf_reader(get_created_vcf_tabix_files):
"""Get all variants from mocked file stream, filter SNPs, multi allele & multi samples
"""
vcf_file_path, tabix_file_path = get_created_vcf_tabix_files(mock_file_input())
vcf_reader = VCFReader(vcf_file_path, bams=[], is_fp=False)
assert(len(vcf_reader) == 17)
def new_vcf_reader_init(self, *args, **kargs):
MockPyVCFReader.original_pyvcf_reader_init_function(
self, mock_file_input())