def test_sv_out_of_range(self):
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr19 88013 . CTT C 20 PASS . GT 0/1\n
chr19 89272 . C T 20 PASS . GT 0/1\n
chr19 269852 . A AAAAGAAAGGCATGACCTATCCACCCATGCCACCTGGATGGACCTCACAGGCACACTGCTTCATGAGAGAG 20 PASS . GT 1/1
"""
pred_io = StringIO.StringIO(pred_str)
pred_vcf = vcf.Reader(pred_io)
stat_reporter = evaluate_low_memory(self.true_vars, pred_vcf, sv_eps, sv_eps, get_reference(),50,50, {'chr19':0,None:100})
self.truePositive(stat_reporter,VARIANT_TYPE.SNP)
self.trueNegative(stat_reporter,VARIANT_TYPE.INDEL_INS)
self.truePositive(stat_reporter,VARIANT_TYPE.INDEL_DEL)
sv_ins_stats = stat_reporter(VARIANT_TYPE.SV_INS)
self.assertEqual(sv_ins_stats['num_true'],1)
self.assertEqual(sv_ins_stats['num_pred'],1)
self.assertEqual(sv_ins_stats['good_predictions'],0)
self.assertEqual(sv_ins_stats['intersect_bad'],0)
self.assertEqual(sv_ins_stats['false_negatives'],1)
self.assertEqual(sv_ins_stats['nrd_total'],0)
self.assertEqual(sv_ins_stats['nrd_wrong'],0)
self.trueNegative(stat_reporter,VARIANT_TYPE.SV_DEL)
def test_false_neg_snp(self):
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr19 88013 . CTT C 20 PASS . GT 0/1\n
chr19 269751 . A AAAAGAAAGGCATGACCTATCCACCCATGCCACCTGGATGGACCTCACAGGCACACTGCTTCATGAGAGAG 20 PASS . GT 1/1
"""
pred_io = StringIO.StringIO(pred_str)
pred_vcf = vcf.Reader(pred_io)
stat_reporter = evaluate_low_memory(self.true_vars, pred_vcf, sv_eps, sv_eps, get_reference(),50,50, {'chr19':0,None:100})
self.falseNegative(stat_reporter,VARIANT_TYPE.SNP)
self.trueNegative(stat_reporter,VARIANT_TYPE.INDEL_INS)
self.truePositive(stat_reporter,VARIANT_TYPE.INDEL_DEL)
self.truePositive(stat_reporter,VARIANT_TYPE.SV_INS)
self.trueNegative(stat_reporter,VARIANT_TYPE.SV_DEL)
def test_perfect(self):
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
##source=TVsim\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr19 88013 . CTT C 20 PASS . GT 0/1\n
chr19 89272 . C T 20 PASS . GT 0/1\n
chr19 269751 . A AAAAGAAAGGCATGACCTATCCACCCATGCCACCTGGATGGACCTCACAGGCACACTGCTTCATGAGAGAG 20 PASS . GT 1/1
"""
pred_io = StringIO.StringIO(pred_str)
pred_vcf = vcf.Reader(pred_io)
#def evaluate_low_memory(true_iter,pred_iter,eps,eps_bp,ref,window,max_indel_len,contig_lookup,writer=None,known_fp_iter=None):
stat_reporter = evaluate_low_memory(self.true_vars, pred_vcf, sv_eps, sv_eps, get_reference(), 50, 50, {'chr19':0,None:100})
self.truePositive(stat_reporter,VARIANT_TYPE.SNP)
self.trueNegative(stat_reporter,VARIANT_TYPE.INDEL_INS)
self.truePositive(stat_reporter,VARIANT_TYPE.INDEL_DEL)
self.truePositive(stat_reporter,VARIANT_TYPE.SV_INS)
self.trueNegative(stat_reporter,VARIANT_TYPE.SV_DEL)