def test_open_cnv_regions(self):
''' test that open_cnv_regions() works correctly
'''
lines = ['id_syndrome_feature\tid_syndrome\tcopy_number\tchr_start\tchr_end\tchr\n',
'20\t1\t1\t1569197\t2110236\t4\tNA\t2650330\t149066\t1t\n']
lines = [ x.encode('utf8') for x in lines ]
self.temp.writelines(lines)
self.temp.flush()
self.assertEqual(open_cnv_regions(self.temp.name),
{('4', '1569197', '2110236'): '1'})
def test_open_cnv_regions(self):
''' test that open_cnv_regions() works correctly
'''
lines = [
'id_syndrome_feature\tid_syndrome\tcopy_number\tchr_start\tchr_end\tchr\n',
'20\t1\t1\t1569197\t2110236\t4\tNA\t2650330\t149066\t1t\n'
]
lines = [x.encode('utf8') for x in lines]
self.temp.writelines(lines)
self.temp.flush()
self.assertEqual(open_cnv_regions(self.temp.name),
{('4', '1569197', '2110236'): '1'})
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 load_definitions_files(self):
"""loads all the config files for the script (eg filters, gene IDs)
"""
# if we have named a gene file, then load a dictionary of genes, and
# add them to the filters, so we can screen variants for being in genes
# known to be involved with disorders
self.known_genes = None
if self.options.genes is not None:
self.known_genes = open_known_genes(self.options.genes)
# if we have named an ID mapping file, the load a dictionary of IDs and
# alternate IDs, so we can convert between different ID schemes.
self.ID_mapper = None
if self.options.alternate_ids is not None:
self.ID_mapper = create_person_ID_mapper(self.options.alternate_ids)
# open a list of regions associated with DECIPHER syndromes
self.cnv_regions = None
if self.options.regions is not None:
self.cnv_regions = open_cnv_regions(self.options.regions)
def load_definitions_files(self):
"""loads all the config files for the script (eg filters, gene IDs)
"""
# if we have named a gene file, then load a dictionary of genes, and
# add them to the filters, so we can screen variants for being in genes
# known to be involved with disorders
self.known_genes = None
if self.options.genes is not None:
self.known_genes = open_known_genes(self.options.genes)
# if we have named an ID mapping file, the load a dictionary of IDs and
# alternate IDs, so we can convert between different ID schemes.
self.ID_mapper = None
if self.options.alternate_ids is not None:
self.ID_mapper = create_person_ID_mapper(
self.options.alternate_ids)
# open a list of regions associated with DECIPHER syndromes
self.cnv_regions = None
if self.options.regions is not None:
self.cnv_regions = open_cnv_regions(self.options.regions)
