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)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
stat_reporter, errors = evaluate_variants(self.true_vars, pred_vars,
sv_eps, sv_eps, None, None,
None)
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_bad_sv_ins(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 AAAAGAAAGGCATGACCTATCCTTTTATGCCACCTGGATGGACCTCACAGGCACACTGCTTCATGAGAGAG 20 PASS . GT 1/1
"""
pred_io = StringIO.StringIO(pred_str)
pred_vcf = vcf.Reader(pred_io)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
sv_eps = 100
stat_reporter, errors = evaluate_variants(self.true_vars, pred_vars,
sv_eps, sv_eps, None, None,
None)
self.truePositive(stat_reporter, VARIANT_TYPE.SNP)
self.trueNegative(stat_reporter, VARIANT_TYPE.INDEL_INS)
self.truePositive(stat_reporter, VARIANT_TYPE.INDEL_DEL)
self.badCallAtTrueSite(stat_reporter, VARIANT_TYPE.SV_INS)
self.trueNegative(stat_reporter, VARIANT_TYPE.SV_DEL)
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)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
stat_reporter, errors = evaluate_variants(self.true_vars, pred_vars, sv_eps, sv_eps, None, None, None)
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)
pred_vars = Variants(pred_vcf, MAX_INDEL_LEN)
stat_reporter, errors = evaluate_variants(self.true_vars, pred_vars, sv_eps, sv_eps, None, None, None)
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_known_false_positives(self):
true_vcf = """##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
chr1 1 . T A 20 PASS . GT 0/1\n
chr1 8 . A C 20 PASS . GT 1/1\n
"""
pred_vcf = """##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
chr1 3 . G C 20 PASS . GT 1/1\n
chr1 5 . C G 20 PASS . GT 0/1\n
chr1 8 . A C 20 PASS . GT 1/1\n
"""
known_fp_vcf = """##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
chr1 3 . G . 20 PASS . GT 0/0\n
chr1 5 . C G 20 PASS . GT 0/0\n
chr1 9 . T . 20 PASS . GT 0/0\n
"""
known_fp_io = StringIO.StringIO(known_fp_vcf)
known_fp_vars = Variants(vcf.Reader(known_fp_io),MAX_INDEL_LEN,knownFP=True)
stat_reporter, vcf_output = evaluate_variants(vcf_to_Variants(true_vcf),vcf_to_Variants(pred_vcf),sv_eps,sv_eps, \
get_reference(),50,known_fp_vars)
snp_stats = stat_reporter(VARIANT_TYPE.SNP)
self.assertEqual(snp_stats['num_true'],2)
self.assertEqual(snp_stats['num_pred'],3)
self.assertEqual(snp_stats['good_predictions'],1)
self.assertEqual(snp_stats['false_positives'],2) # predicted vars not in ground truth
self.assertEqual(snp_stats['false_negatives'],1)
self.assertEqual(snp_stats['known_fp_calls'],2)
self.assertEqual(snp_stats['known_fp'],2)