def test__save_tabular(self):
''' check that _save_tabular() works correctly
'''
temp = tempfile.NamedTemporaryFile(suffix='.txt',
dir=self.temp_dir,
delete=False)
report = Report(temp.name, None, None)
var = (self.variants[0], ["single_variant"], ["Monoallelic"], ["TEST"])
var[0].child.format['GQ'] = 40
_save_tabular(temp.name, [var], self.trio)
with open(temp.name, 'r') as handle:
lines = handle.readlines()
expected = [
'proband\tsex\tchrom\tposition\tgene\t'
'mutation_ID\ttranscript\tconsequence\tref/alt_alleles\tMAX_MAF\t'
'inheritance\ttrio_genotype\tmom_aff\tdad_aff\tresult\tpp_dnm\t'
'exac_allele_count\tGQ\thas_parents\tcnv_length\n',
'child\tF\tX\t150\tTEST\tNA\tNA\t'
'missense_variant\tA/G\t0.0005\tMonoallelic\t1/0/0\t1\t1\t'
'single_variant\t0.99\tNA\t40\tTrue\tNA\n'
]
self.assertEqual(lines, expected)
def setUp(self):
""" define a family and variant, and start the Allosomal class
"""
# generate a test family
child_gender = "F"
mom_aff = "1"
dad_aff = "1"
self.trio = self.create_family(child_gender, mom_aff, dad_aff)
# generate a test variant
child = create_snv(child_gender,
"0/1",
chrom='X',
pos=150,
extra_info='HGNC=TEST;MAX_AF=0.0005')
mom = create_snv("F", "0/0", chrom='X', pos=150)
dad = create_snv("M", "0/0", chrom='X', pos=150)
self.variants = [TrioGenotypes('X', '150', child, mom, dad)]
self.report = Report(None, None, None)
Info.set_populations([
"AFR_AF", "AMR_AF", "ASN_AF", "DDD_AF", "EAS_AF", "ESP_AF",
"EUR_AF", "MAX_AF", "SAS_AF", "UK10K_cohort_AF"
])
def __init__(self, opts):
"""intialise the class with the some definitions
"""
self.set_definitions(opts)
self.report = Report(self.output_path, self.export_vcf, self.ID_mapper,
self.known_genes_date)
def __init__(self, population_tags=None, count=0, known_genes=None, date=None,
regions=None, lof_sites=None, pp_filter=0.0, sum_x_lr2_file=None,
output_path=None, export_vcf=None, debug_chrom=None, debug_pos=None):
""" initialise the class object
Args:
population_tags: list of population ID tags, that could exist within
the INFO field, or None.
count: number of probands to analyse, helpful for tracking progress
in output logs.
known_genes: path to table of genes genes known to be associated
with genetic disorders, or None.
date: date of the known_genes file, or None if not using/unknown.
regions: path to a table of regions for DECIPHER CNV syndromes.
lof_sites: path to json file of [chrom, position] coordinates in
genome, for modifying to a loss-of-function consequence if
required. Can be None if unneeded.
pp_filter: threshold from 0 to 1 for pp_dnm value to filter out
candidiate DNMs which fall below this value
sum_x_lr2_file: File containing sum of l2r values on x chromosome
for each person
output_path: path to write output tab-separated file to
export_vcf: path to file or folder to write VCFs to.
debug_chrom: chromosome for debugging purposes.
debug_pos: position for debugging variant filtering at.
"""
self.pp_filter = pp_filter
self.total = count
self.count = 0
self.populations = population_tags
self.debug_chrom = debug_chrom
self.debug_pos = debug_pos
# open reference datasets, these return None if the paths are None
self.known_genes = open_known_genes(known_genes)
self.cnv_regions = open_cnv_regions(regions)
self.last_base = open_last_base_sites(lof_sites)
#open file containing sum of mean log 2 ratios on X, returns an empty dict if path is None
self.sum_x_lr2 = open_x_lr2_file(sum_x_lr2_file)
self.reporter = Report(output_path, export_vcf, date)
def setUp(self):
""" define a family and variant, and start the Allosomal class
"""
# generate a test family
child_gender = "F"
mom_aff = "1"
dad_aff = "1"
self.trio = self.create_family(child_gender, mom_aff, dad_aff)
# generate a test variant
child_var = self.create_snv(child_gender, "0/1")
mom_var = self.create_snv("F", "0/0")
dad_var = self.create_snv("M", "0/0")
var = TrioGenotypes(child_var)
var.add_mother_variant(mom_var)
var.add_father_variant(dad_var)
self.variants = [var]
self.report = Report(None, None, None, None)
self.report.family = self.trio
