def test_export_family_xls4(self):
"""
to check if mutation annotation from families
with several alternate alleles is correctly exported
"""
self.individual_debug = True
self.init_test(self.current_func_name)
ma = self.__create_xls_instance()
test_sa_file = os.path.join(self.data_dir,
self.current_func_name + '.tab.csv')
test_vcf_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_chrom = 18
test_begin_pos = 12512309
test_end_pos = 14513570
test_fam_file = os.path.join(self.data_dir,
self.current_func_name + '.txt')
db_man = DBManager()
db_man.connect_summarize_annovar_db(test_sa_file)
db_man.connect_vcf_db(test_vcf_file, test_chrom, test_begin_pos, test_end_pos)
db_man.connect_family_db(test_fam_file)
ma.db_manager = db_man
ma.export_family_xls('91', self.working_dir)
ma.export_family_xls('296', self.working_dir)
def test_export_family_xls5(self):
"""
for almost real data, to check if mutation annotation
from one family is correctly exported
"""
self.individual_debug = True
self.init_test(self.current_func_name)
ma = self.__create_xls_instance('chr18')
test_sa_file = os.path.join(self.data_dir,
self.current_func_name + '.tab.csv')
test_vcf_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_chrom = 18
test_begin_pos = 10707433
test_end_pos = 20607819
test_fam_file = os.path.join(self.data_dir,
self.current_func_name + '.txt')
db_man = DBManager()
db_man.connect_summarize_annovar_db(test_sa_file)
db_man.connect_vcf_db(test_vcf_file, test_chrom, test_begin_pos, test_end_pos)
db_man.connect_family_db(test_fam_file)
ma.db_manager = db_man
ma.export_family_xls('918', self.working_dir)
ma.export_family_xls('8', self.working_dir)
def export_xls_pos(
chrom,
begin_pos,
end_pos,
sa_tab_csv_file,
vcf_tabix_file,
family_file,
output_dir,
report_code=None,
):
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if report_code is None:
report_code = 'chr' + str(chrom)
ma = MutationAnnotator(report_code)
db_man = DBManager()
db_man.connect_summarize_annovar_db(sa_tab_csv_file)
db_man.connect_vcf_db(vcf_tabix_file, chrom, begin_pos, end_pos)
db_man.connect_family_db(family_file)
ma.db_manager = db_man
ma.export_xls(output_dir)
def test_annotate_group_stat2(self):
"""
to check if the group stat calculation is correct
if number of patients in family file is not equal to that in vcf
"""
self.init_test(self.current_func_name)
ma = self.__create_xls_instance()
test_sa_file = os.path.join(self.data_dir,
self.current_func_name + '.tab.csv')
test_vcf_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_chrom = 18
test_begin_pos = 11853000
test_end_pos = 11854000
test_fam_file = os.path.join(self.data_dir,
self.current_func_name + '.txt')
db_man = DBManager()
db_man.connect_summarize_annovar_db(test_sa_file)
db_man.connect_vcf_db(test_vcf_file, test_chrom, test_begin_pos, test_end_pos)
db_man.connect_family_db(test_fam_file)
ma.db_manager = db_man
test_mutation = ma.vcf_mutations['18|11853053']
self.assertEqual(test_mutation.stats_type1_ac,
[28],
'Incorrect type1 allele count')
self.assertEqual(test_mutation.stats_type1_pc,
[14],
'Incorrect type1 patient count')
self.assertEqual(test_mutation.stats_type1_pp,
[1],
'Incorrect type1 patient percentage')
self.assertEqual(test_mutation.stats_type1_gc,
14,
'Incorrect type1 genotype count')
self.assertEqual(test_mutation.stats_type1_gp,
1,
'Incorrect type1 genotype percentage')
def export_xls_pos(
sa_tab_csv_file,
vcf_tabix_file,
family_file,
output_dir,
report_code=None,
chrom="",
begin_pos="",
end_pos="",
patient_codes=None,
):
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if report_code is None:
report_code = "chr" + str(chrom)
ma = MutationAnnotator(report_code)
db_man = DBManager()
db_man.connect_summarize_annovar_db(sa_tab_csv_file)
db_man.connect_vcf_db(vcf_tabix_file, chrom, begin_pos, end_pos, patient_codes=patient_codes)
db_man.connect_family_db(family_file)
ma.db_manager = db_man
ma.export_xls(output_dir)
def test_export_family_with_exon_filter(self):
self.individual_debug = True
self.init_test(self.current_func_name)
ma = self.__create_xls_instance()
test_sa_file = os.path.join(self.data_dir,
self.current_func_name + '.tab.csv')
test_vcf_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_chrom = ""
test_begin_pos = 12512309
test_end_pos = 14513570
test_fam_file = os.path.join(self.data_dir,
self.current_func_name + '.txt')
db_man = DBManager()
self.dbg("export family xls4: before connect summarize annovar")
db_man.connect_summarize_annovar_db(test_sa_file)
self.dbg("export family xls4: before connect vcf db")
db_man.connect_vcf_db(test_vcf_file, test_chrom, test_begin_pos, test_end_pos)
self.dbg("export family xls4: before connect family db")
db_man.connect_family_db(test_fam_file)
ma.db_manager = db_man
ma.export_family_xls('91', self.working_dir)
ma.export_family_xls('296', self.working_dir)
def test_annotate_group_stat1(self):
""" to check if the group stat calculation is correct"""
self.init_test(self.current_func_name)
ma = self.__create_xls_instance()
test_sa_file = os.path.join(self.data_dir,
self.current_func_name + '.tab.csv')
test_vcf_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_chrom = 18
test_begin_pos = 12789246
test_end_pos = 12793745
test_fam_file = os.path.join(self.data_dir,
self.current_func_name + '.txt')
db_man = DBManager()
db_man.connect_summarize_annovar_db(test_sa_file)
db_man.connect_vcf_db(test_vcf_file, test_chrom, test_begin_pos, test_end_pos)
db_man.connect_family_db(test_fam_file)
ma.db_manager = db_man
test_mutation = ma.vcf_mutations['18|12793222']
self.assertEqual(test_mutation.stats_type1_ac,
[16],
'Incorrect type1 allele count')
self.assertEqual(test_mutation.stats_type1_pc,
[12],
'Incorrect type1 patient count')
self.assertEqual(test_mutation.stats_type1_pp,
[0.32],
'Incorrect type1 patient percentage')
self.assertEqual(test_mutation.stats_type1_gc,
37,
'Incorrect type1 genotype count')
self.assertEqual(test_mutation.stats_type1_gp,
0.49,
'Incorrect type1 genotype percentage')
self.assertEqual(test_mutation.stats_type2_ac,
[14],
'Incorrect type2 allele count')
self.assertEqual(test_mutation.stats_type2_pc,
[10],
'Incorrect type2 patient count')
self.assertEqual(test_mutation.stats_type2_pp,
[0.42],
'Incorrect type2 patient percentage')
self.assertEqual(test_mutation.stats_type2_gc,
24,
'Incorrect type2 genotype count')
self.assertEqual(test_mutation.stats_type2_gp,
0.65,
'Incorrect type2 genotype percentage')
self.assertEqual(test_mutation.stats_type3_ac,
[1],
'Incorrect type3 allele count')
self.assertEqual(test_mutation.stats_type3_pc,
[1],
'Incorrect type3 patient count')
self.assertEqual(test_mutation.stats_type3_pp,
[0.1],
'Incorrect type3 patient percentage')
self.assertEqual(test_mutation.stats_type3_gc,
10,
'Incorrect type3 genotype count')
self.assertEqual(test_mutation.stats_type3_gp,
0.48,
'Incorrect type3 genotype percentage')
self.assertEqual(test_mutation.stats_type4_ac,
[6],
'Incorrect type4 allele count')
self.assertEqual(test_mutation.stats_type4_pc,
[4],
'Incorrect type4 patient count')
self.assertEqual(test_mutation.stats_type4_pp,
[0.57],
'Incorrect type4 patient percentage')
self.assertEqual(test_mutation.stats_type4_gc,
7,
'Incorrect type4 genotype count')
self.assertEqual(test_mutation.stats_type4_gp,
0.19,
'Incorrect type4 genotype percentage')
def test_annotate_group_stat3(self):
"""
to check if the group stat calculation is correct
if there are several alternate alleles
"""
self.init_test(self.current_func_name)
ma = self.__create_xls_instance()
test_sa_file = os.path.join(self.data_dir,
self.current_func_name + '.tab.csv')
test_vcf_file = os.path.join(self.data_dir,
self.current_func_name + '.vcf.gz')
test_chrom = 18
test_begin_pos = 12512309
test_end_pos = 14513570
test_fam_file = os.path.join(self.data_dir,
self.current_func_name + '.txt')
db_man = DBManager()
db_man.connect_summarize_annovar_db(test_sa_file)
db_man.connect_vcf_db(test_vcf_file, test_chrom, test_begin_pos, test_end_pos)
db_man.connect_family_db(test_fam_file)
ma.db_manager = db_man
test_mutation = ma.vcf_mutations['18|12512385']
self.assertEqual(test_mutation.stats_type1_ac,
[34, 31],
'Incorrect type1 allele count')
self.assertEqual(test_mutation.stats_type1_pc,
[23, 23],
'Incorrect type1 patient count')
self.assertEqual(test_mutation.stats_type1_pp,
[0.4, 0.4],
'Incorrect type1 patient percentage')
self.assertEqual(test_mutation.stats_type1_gc,
57,
'Incorrect type1 genotype count')
self.assertEqual(test_mutation.stats_type1_gp,
0.75,
'Incorrect type1 genotype percentage')
test_mutation = ma.vcf_mutations['18|14513526']
self.assertEqual(test_mutation.stats_type1_ac,
[15],
'Incorrect type1 allele count')
self.assertEqual(test_mutation.stats_type1_pc,
[13],
'Incorrect type1 patient count')
self.assertEqual(test_mutation.stats_type1_pp,
[0.34],
'Incorrect type1 patient percentage')
self.assertEqual(test_mutation.stats_type1_gc,
38,
'Incorrect type1 genotype count')
self.assertEqual(test_mutation.stats_type1_gp,
0.5,
'Incorrect type1 genotype percentage')
test_mutation = ma.vcf_mutations['18|14513535']
self.assertEqual(test_mutation.stats_type1_ac,
[18, 27, 15],
'Incorrect type1 allele count')
self.assertEqual(test_mutation.stats_type1_pc,
[11, 21, 9],
'Incorrect type1 patient count')
self.assertEqual(test_mutation.stats_type1_pp,
[0.26, 0.5, 0.21],
'Incorrect type1 patient percentage')
self.assertEqual(test_mutation.stats_type1_gc,
42,
'Incorrect type1 genotype count')
self.assertEqual(test_mutation.stats_type1_gp,
0.55,
'Incorrect type1 genotype percentage')