def testRectify2(self):
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . GC G 20 PASS . GT 1/1\n
chr2 6 . G A 20 PASS . GT 1/1\n
"""
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . GCCG GCA 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr2')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr2')
gtdict = _genotype_concordance_dict()
cvs = ChromVariantStats(true_vars, pred_vars, [], [3, 6], [3], gtdict)
cvs.rectify(get_reference(), 100)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_OTH], 1)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_OTH], 1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_OTH], 0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_OTH], 0)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.SNP], 0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP], 0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP], 0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP], 0)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_DEL], 0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL], 0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL], 0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL], 0)
def testTruePosRectify(self):
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 3 . TC T 20 PASS . GT 1/1\n
chr4 5 . TC T 20 PASS . GT 1/1\n
chr4 8 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 4 . C T 20 PASS . GT 1/1\n
chr4 5 . TC T 20 PASS . GT 1/1\n
chr4 7 . TC T 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr4')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr4')
gtdict = _genotype_concordance_dict()
cvs = ChromVariantStats(true_vars, pred_vars, [5], [4, 7], [3, 8],
gtdict)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP], 0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP], 1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP], 1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL], 1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL], 1)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL], 1)
cvs.rectify(get_reference(), 100)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP], 0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP], 0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP], 1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL], 0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL], 2)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL], 0)
def testInit(self):
# test counts of false positive, false negative, true positive
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 5 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 7 . G C 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr2')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr2')
gtdict = _genotype_concordance_dict()
gtdict[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][
GENOTYPE_TYPE.HOM_VAR] += 1
cvs = ChromVariantStats(true_vars, pred_vars, [3], [7], [5], gtdict)
self.assertEqual(cvs.num_true[VARIANT_TYPE.SNP], 2)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.SNP], 2)
self.assertEqual(len(cvs.false_positives.all_locations), 1)
self.assertEqual(len(cvs.false_negatives.all_locations), 1)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP], 1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP], 1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP], 1)
def testRectify(self):
# rectify CVS with a rescue-able indel
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 2 . TGC TAT 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 4 . C T 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr2')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr2')
gtdict = _genotype_concordance_dict(
) # leave empty, we aren't testing this yet
cvs = ChromVariantStats(true_vars, pred_vars, [], [3, 4], [2], gtdict)
# before rectify, no true positives
self.assertTrue(all(map(lambda x: x == 0, cvs.num_tp.itervalues())))
# one false negative indel
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_OTH], 1)
# two false positives SNPs
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP], 2)
cvs.rectify(get_reference(), 100)
# after rectify, one true positive indel
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_OTH], 1)
# no false positives or false negatives
self.assertTrue(all(map(lambda x: x == 0, cvs.num_fp.itervalues())))
self.assertTrue(all(map(lambda x: x == 0, cvs.num_fn.itervalues())))
def testTruePosRectify(self):
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 3 . TC T 20 PASS . GT 1/1\n
chr4 5 . TC T 20 PASS . GT 1/1\n
chr4 8 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 4 . C T 20 PASS . GT 1/1\n
chr4 5 . TC T 20 PASS . GT 1/1\n
chr4 7 . TC T 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr4')
pred_vars = vcf_to_ChromVariants(pred_str,'chr4')
gtdict = _genotype_concordance_dict()
cvs = ChromVariantStats(true_vars,pred_vars,[5],[4,7],[3,8],gtdict)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],1)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],1)
cvs.rectify(get_reference(),100)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],2)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],0)
def testRectify2(self):
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . GC G 20 PASS . GT 1/1\n
chr2 6 . G A 20 PASS . GT 1/1\n
"""
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . GCCG GCA 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr2')
pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
gtdict = _genotype_concordance_dict()
cvs = ChromVariantStats(true_vars, pred_vars, [], [3,6], [3],gtdict)
cvs.rectify(get_reference(),100)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_OTH],1)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_OTH],1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_OTH],0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_OTH],0)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.SNP],0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],0)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.INDEL_DEL],0)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],0)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],0)
def testRectify(self):
# rectify CVS with a rescue-able indel
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 2 . TGC TAT 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 4 . C T 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr2')
pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
gtdict = _genotype_concordance_dict() # leave empty, we aren't testing this yet
cvs = ChromVariantStats(true_vars,pred_vars,[],[3,4],[2],gtdict)
# before rectify, no true positives
self.assertTrue(all(map(lambda x: x == 0,cvs.num_tp.itervalues())))
# one false negative indel
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_OTH],1)
# two false positives SNPs
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],2)
cvs.rectify(get_reference(),100)
# after rectify, one true positive indel
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_OTH],1)
# no false positives or false negatives
self.assertTrue(all(map(lambda x: x == 0, cvs.num_fp.itervalues())))
self.assertTrue(all(map(lambda x: x ==0, cvs.num_fn.itervalues())))
def testInit(self):
# test counts of false positive, false negative, true positive
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 5 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 7 . G C 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr2')
pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
gtdict = _genotype_concordance_dict()
gtdict[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][GENOTYPE_TYPE.HOM_VAR] += 1
cvs = ChromVariantStats(true_vars,pred_vars,[3],[7],[5],gtdict)
self.assertEqual(cvs.num_true[VARIANT_TYPE.SNP],2)
self.assertEqual(cvs.num_pred[VARIANT_TYPE.SNP],2)
self.assertEqual(len(cvs.false_positives.all_locations),1)
self.assertEqual(len(cvs.false_negatives.all_locations),1)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SNP],1)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.SNP],1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],1)
def testAggregate(self):
# build two ChromVariantStats objects
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 5 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 7 . G C 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr2')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr2')
gtdict = _genotype_concordance_dict() # leave empty for now
cvs2 = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr3 3 . G A 20 PASS . GT 1/1\n
chr3 5 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr3 3 . G A 20 PASS . GT 1/1\n
chr3 4 . T A 20 PASS . GT 1/1\n
chr3 7 . G C 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr3')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr3')
cvs3 = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
#cvs5 = ChromVariantStats(true_vars,pred_vars,[31],[49,79],[52],_genotype_concordance_dict())
aggregator, errors = _aggregate([cvs2, cvs3])
# test some sums
self.assertEqual(cvs2.num_true[VARIANT_TYPE.SNP], 2)
self.assertEqual(cvs3.num_true[VARIANT_TYPE.SNP], 2)
self.assertEqual(aggregator(VARIANT_TYPE.SNP)['num_true'], 4)
self.assertEqual(cvs2.num_tp[VARIANT_TYPE.SNP], 1)
self.assertEqual(cvs3.num_tp[VARIANT_TYPE.SNP], 1)
self.assertEqual(aggregator(VARIANT_TYPE.SNP)['good_predictions'], 2)
def testAggregate(self):
# build two ChromVariantStats objects
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 5 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 3 . G A 20 PASS . GT 1/1\n
chr2 7 . G C 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr2')
pred_vars = vcf_to_ChromVariants(pred_str,'chr2')
gtdict = _genotype_concordance_dict() # leave empty for now
cvs2 = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
true_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr3 3 . G A 20 PASS . GT 1/1\n
chr3 5 . C T 20 PASS . GT 1/1\n
"""
pred_str = """##fileformat=VCFv4.0\n
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr3 3 . G A 20 PASS . GT 1/1\n
chr3 4 . T A 20 PASS . GT 1/1\n
chr3 7 . G C 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr3')
pred_vars = vcf_to_ChromVariants(pred_str,'chr3')
cvs3 = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
#cvs5 = ChromVariantStats(true_vars,pred_vars,[31],[49,79],[52],_genotype_concordance_dict())
aggregator,errors = _aggregate([cvs2,cvs3])
# test some sums
self.assertEqual(cvs2.num_true[VARIANT_TYPE.SNP],2)
self.assertEqual(cvs3.num_true[VARIANT_TYPE.SNP],2)
self.assertEqual(aggregator(VARIANT_TYPE.SNP)['num_true'],4)
self.assertEqual(cvs2.num_tp[VARIANT_TYPE.SNP],1)
self.assertEqual(cvs3.num_tp[VARIANT_TYPE.SNP],1)
self.assertEqual(aggregator(VARIANT_TYPE.SNP)['good_predictions'],2)
