def test_process_1():
"""
tests the 100% edited filter
:return:
"""
alfa = 0
beta = 0
cov_margin = 0.01
with open('vcf/rank_edit_variant_1.eff', 'r') as f:
line = f.readline()
output_string = r.process(alfa, beta, cov_margin, True, line)
output_string = output_string.split('\t')
assert output_string[8] == 'PASS'
output_string = r.process(alfa, beta, cov_margin, False, line)
output_string = output_string.split('\t')
assert output_string[8] == 'POSSIBLE_SNP'
def test_process_4():
"""
tests the standard conf score (a = G, b = A)
:return:
"""
from scipy.special import betainc
a = 0 # pseudocount
b = 0 # pseudocount
cov_margin = 0.01
total_coverage = 5
dp4 = '4,0,1,0'
fraction = 0.2
# confidence = 1 - betainc(G, A, cov_margin)
keep_all_edited = False
test_vcf_line = 'chrI 15542 {} A G {} . DP={};DPR=4,1;SGB=-0.379885;RPB=1;MQB=1;BQB=1;MQ0F=0;AF1=0.406103;AC1=1;DP4={};MQ=20;FQ=-29.53;PV4=1,1,1,1 GT:PL:DP:DV:SP:DP4:DPR 0/0:5,0,47:5:1:0:0,4,0,1:4,1'.format(
total_coverage, fraction, total_coverage, dp4)
result_line = r.process(a, b, cov_margin, keep_all_edited, test_vcf_line)
result_line = result_line.split('\t')
assert result_line[5] == '0.96059601'
