def testLeftNormalize(self):
#left normalize deletion
norm_pos, norm_ref, norm_alts = left_normalize(get_reference(),'chr1',2,'CGCCG',['CG'])
self.assertEqual(norm_pos,0)
self.assertEqual(norm_ref,'AACGC')
self.assertEqual(norm_alts[0],'AA')
#left normalize insertion
norm_pos, norm_ref, norm_alts = left_normalize(get_reference(),'chr4',12,'G',['GGG'])
self.assertEqual(norm_pos,7)
self.assertEqual(norm_ref,'C')
self.assertEqual(norm_alts[0],'CGG')
def testChromEvaluateGenotypeConcordance(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
chr1 2 . A T 20 PASS . GT 0/1\n
chr1 5 . C T 20 PASS . GT 0/1\n
chr1 9 . A G 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
chr1 2 . A T 20 PASS . GT 1/1\n
chr1 6 . C G 20 PASS . GT 0/1\n
chr1 9 . A G 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr1')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr1')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
self.assertEqual(
cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HET][
GENOTYPE_TYPE.HOM_VAR], 1)
self.assertEqual(
cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][
GENOTYPE_TYPE.HOM_VAR], 1)
# anything other than TP don't get counted in genotype concordance
self.assertEqual(cvs._nrd_counts(VARIANT_TYPE.SNP), (1, 2))
# phased variants should be counted correctly
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
chr1 2 . A T 20 PASS . GT 0|1\n
chr1 9 . A G 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
chr1 2 . A T 20 PASS . GT 1|0\n
chr1 9 . A G 20 PASS . GT 1|1\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr1')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr1')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
self.assertEqual(
cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HET][
GENOTYPE_TYPE.HET], 1)
self.assertEqual(
cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][
GENOTYPE_TYPE.HOM_VAR], 1)
self.assertEqual(cvs._nrd_counts(VARIANT_TYPE.SNP), (0, 2))
def testLeftNormalize(self):
#left normalize deletion
norm_pos, norm_ref, norm_alts = left_normalize(get_reference(), 'chr1',
2, 'CGCCG', ['CG'])
self.assertEqual(norm_pos, 0)
self.assertEqual(norm_ref, 'AACGC')
self.assertEqual(norm_alts[0], 'AA')
#left normalize insertion
norm_pos, norm_ref, norm_alts = left_normalize(get_reference(), 'chr2',
4, 'CGGA', ['CTTGGA'])
self.assertEqual(norm_pos, 1)
self.assertEqual(norm_ref, 'TGCC')
self.assertEqual(norm_alts[0], 'TGCCTT')
def testChromEvaluateVariantsSV(self):
#NB: SVs aren't rescued, just checked for within breakpoint tolerance
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
chr1 6 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
#SV with exact position, exact allele match
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
chr1 6 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr1')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr1')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS], 1)
#SV with exact position, difference allele match
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
chr1 6 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAATGC 20 PASS . GT 0/1
"""
pred_vars = vcf_to_ChromVariants(pred_str, 'chr1')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS], 1)
#SV with position within tolerance, exact allele match
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
chr1 4 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
pred_vars = vcf_to_ChromVariants(pred_str, 'chr1')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS], 1)
#SV outside of tolerance
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
chr1 110 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
pred_vars = vcf_to_ChromVariants(pred_str, 'chr1')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS], 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 testRescueChromEvalVariants(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')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
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 testTooManyPaths(self):
fn_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
chr1 10049 . CTTAAGCT C 20 PASS . GT 1/1\n
chr1 10053 . TGCGT T 20 PASS . GT 0/1\n
chr1 10055 . GCTAA G 20 PASS . GT 0/1\n
chr1 10057 . TA T 20 PASS . GT 1/1\n
chr1 10058 . GC G 20 PASS . GT 1/1\n
"""
fp_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
chr1 10025 . CTTAAGCT C 20 PASS . GT 1/1\n
chr1 10028 . TGCGT T 20 PASS . GT 0/1\n
chr1 10029 . GCTAA G 20 PASS . GT 0/1\n
chr1 10032 . TA T 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str, 'chr1')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr1')
rescuer = SequenceRescuer('chr1', 10000, fn_vars, fp_vars,
get_empty_ChromVariants('chr2'),
get_reference(), 50)
self.assertFalse(rescuer.rescued)
def testChromEvaluateVariantsKnownFP(self):
# one known true variant
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
chr1 2 . A T 20 PASS . GT 0/1\n
"""
# call var where known fp is, where true var is, where nothing is known
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
chr1 2 . A T 20 PASS . GT 0/1\n
chr1 4 . G C 20 PASS . GT 1/1\n
chr1 7 . G A 20 PASS . GT 0/1\n
"""
# known locations with NO variant
known_fp_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
chr1 1 . A T 20 PASS . GT ./.\n
chr1 7 . G . 20 PASS . GT 0/0\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr1')
pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
known_fp_io = StringIO.StringIO(known_fp_str)
known_fp = Variants(vcf.Reader(known_fp_io),MAX_INDEL_LEN,knownFP=True)
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50,known_fp.on_chrom('chr1'))
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],2) # usual definition, in pred vars but not in true
self.assertEqual(cvs.calls_at_known_fp[VARIANT_TYPE.SNP],1) # call at location known to NOT have SNP
def testTruePosRescueMission(self):
fn_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 8 . C T 20 PASS . GT 1/1\n
"""
fp_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 7 . TC T 20 PASS . GT 1/1\n
"""
tp_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 5 . TC T 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str, 'chr4')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr4')
tp_vars = vcf_to_ChromVariants(tp_str, 'chr4')
num_new_tp, num_removed_fn = rescue_mission(fn_vars, fp_vars, tp_vars,
3, get_reference(), 100)
self.assertEqual(num_new_tp[VARIANT_TYPE.SNP], 1)
self.assertEqual(num_new_tp[VARIANT_TYPE.INDEL_DEL], 1)
self.assertEqual(num_removed_fn[VARIANT_TYPE.SNP], 1)
self.assertEqual(num_removed_fn[VARIANT_TYPE.INDEL_DEL], 1)
self.assertFalse(fn_vars.all_locations)
self.assertFalse(fp_vars.all_locations)
def testGetSeq(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
chr3 2 . TCGA T 20 PASS . GT 1/1\n
chr3 9 . A AAAA 20 PASS . GT 0/1\n
"""
variants = vcf_to_ChromVariants(pred_str,'chr3')
window_tup = (1,13,'chr3')
sequence = _get_seq(window_tup,variants.getAllVariants(),get_reference(),False)
self.assertEqual(sequence[0],'ATTCGAAAATCG')
self.assertEqual(sequence[1],'')
sequence = _get_seq(window_tup,variants.getAllVariants(),get_reference(),True)
self.assertEqual(sequence[0],'ATTCGATCG')
self.assertEqual(sequence[1],'ATCGATCGAAAATCG')
def testChromEvaluateVariantsKnownFP(self):
# one known true variant
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
chr1 2 . A T 20 PASS . GT 0/1\n
"""
# call var where known fp is, where true var is, where nothing is known
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
chr1 2 . A T 20 PASS . GT 0/1\n
chr1 4 . G C 20 PASS . GT 1/1\n
chr1 7 . G A 20 PASS . GT 0/1\n
"""
# known locations with NO variant
known_fp_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
chr1 1 . A T 20 PASS . GT ./.\n
chr1 7 . G . 20 PASS . GT 0/0\n
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr1')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr1')
known_fp_io = StringIO.StringIO(known_fp_str)
known_fp = Variants(vcf.Reader(known_fp_io),
MAX_INDEL_LEN,
knownFP=True)
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50,
known_fp.on_chrom('chr1'))
self.assertEqual(cvs.num_fp[VARIANT_TYPE.SNP],
2) # usual definition, in pred vars but not in true
self.assertEqual(cvs.calls_at_known_fp[VARIANT_TYPE.SNP],
1) # call at location known to NOT have SNP
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 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 testRescueChromEvalVariants(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')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
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 testChromEvaluateVariantsSV(self):
#NB: SVs aren't rescued, just checked for within breakpoint tolerance
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
chr1 6 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
#SV with exact position, exact allele match
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
chr1 6 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
true_vars = vcf_to_ChromVariants(true_str,'chr1')
pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
#SV with exact position, difference allele match
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
chr1 6 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAATGC 20 PASS . GT 0/1
"""
pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
#SV with position within tolerance, exact allele match
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
chr1 4 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],1)
#SV outside of tolerance
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
chr1 110 . C CGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGACGTGAGATGAAAAA 20 PASS . GT 0/1
"""
pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.SV_INS],0)
def normalizeStringToWriter(self,vcf_str):
vcf_io = StringIO.StringIO(vcf_str)
test_vcf = vcf.Reader(vcf_io)
output_io = StringIO.StringIO()
output_writer = VCFWriter('ref.fasta','name',output_io)
map(lambda r: write(r,output_writer),normalize(get_reference(),test_vcf))
outputStr = output_io.getvalue()
outputStr = outputStr.replace('\n','\n\n')
return vcf.Reader(StringIO.StringIO(outputStr))
def testNBaseNormalization(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 2 . A ATCTT 20 PASS . GT 0/1\n
chr4 3 . NN N 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
self.assertEqual(self.countRecords(norm_iter),1)
def testNBaseNormalization(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 2 . A ATCTT 20 PASS . GT 0/1\n
chr4 3 . NN N 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(), self.getVcf(vcf_str))
self.assertEqual(self.countRecords(norm_iter), 1)
def testGetSeq(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
chr3 2 . TCGA T 20 PASS . GT 1/1\n
chr3 9 . A AAAA 20 PASS . GT 0/1\n
"""
variants = vcf_to_ChromVariants(pred_str, 'chr3')
window_tup = (1, 13, 'chr3')
sequence = _get_seq(window_tup, variants.getAllVariants(),
get_reference(), False)
self.assertEqual(sequence[0], 'ATTCGAAAATCG')
self.assertEqual(sequence[1], '')
sequence = _get_seq(window_tup, variants.getAllVariants(),
get_reference(), True)
self.assertEqual(sequence[0], 'ATTCGATCG')
self.assertEqual(sequence[1], 'ATCGATCGAAAATCG')
def testFullRescue(self):
fn_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
"""
fp_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
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr2')
fp_vars = vcf_to_ChromVariants(fp_str,'chr2')
rescuer = SequenceRescuer('chr2',2,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
self.assertTrue(rescuer.rescued)
self.assertEqual(rescuer.windowsRescued,(0,0))
fp_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
"""
fn_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
"""
fp_vars = vcf_to_ChromVariants(fp_str,'chr2')
fn_vars = vcf_to_ChromVariants(fn_str,'chr2')
rescuer = SequenceRescuer('chr2',3,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
self.assertTrue(rescuer.rescued)
fn_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 8 . C T 20 PASS . GT 1/1\n
"""
fp_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 7 . TC T 20 PASS . GT 1/1\n
"""
tp_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 5 . TC T 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr4')
fp_vars = vcf_to_ChromVariants(fp_str,'chr4')
tp_vars = vcf_to_ChromVariants(tp_str,'chr4')
rescuer = SequenceRescuer('chr4',3,fn_vars,fp_vars,tp_vars,get_reference(),50)
self.assertTrue(rescuer.rescued)
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 testCollidingVariants(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr1 5 . A TGC 20 PASS . GT 1/1\n
chr1 5 . A GGG 20 PASS . GT 1/1\n
"""
norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
count = self.countRecords(norm_iter)
self.assertEqual(count,1)
def testCollidingVariants(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr1 5 . A TGC 20 PASS . GT 1/1\n
chr1 5 . A GGG 20 PASS . GT 1/1\n
"""
norm_iter = normalize(get_reference(), self.getVcf(vcf_str))
count = self.countRecords(norm_iter)
self.assertEqual(count, 1)
def testNormalizedToCollision(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 4 . C T 20 PASS . GT 0/1\n
chr2 5 . C CGC 20 PASS . GT 0/1\n
chr4 2 . A AGG 20 PASS . GT 0/1\n
chr4 6 . C CTC 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(), self.getVcf(vcf_str))
r1 = norm_iter.next()
r2 = norm_iter.next()
r3 = norm_iter.next()
r4 = norm_iter.next()
self.assertEqual(r1.POS, 4) # chr2 SNP doesn't change
self.assertEqual(
r2.POS, 5
) # chr2 insertion gets normed forward 1 base and slid back to original pos
self.assertEqual(r2.REF, "C")
self.assertEqual(r2.ALT, ["CGC"])
self.assertEqual(r3.POS, 2)
self.assertEqual(r3.REF, "A")
self.assertEqual(r3.ALT, ["AGG"])
self.assertEqual(r4.POS, 3)
self.assertEqual(r4.REF, "T")
self.assertEqual(r4.ALT, ["TCT"])
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 2 . ATC A 20 PASS . GT 0/1\n
chr4 6 . CTC C 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(), self.getVcf(vcf_str))
r1 = norm_iter.next()
r2 = norm_iter.next()
self.assertEqual(r1.POS, 2)
self.assertEqual(r1.REF, "ATC")
self.assertEqual(r1.ALT, ["A"])
self.assertEqual(r2.POS, 5)
self.assertEqual(r2.REF, "TCT")
self.assertEqual(r2.ALT, ["T"])
def testGenotypes(self):
# keep genotype info for a compound heterozygous call
vcf_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
chr1 2 . A C,T 20 PASS . GT 1/2\n
"""
vcf = self.getVcf(vcf_str)
record = normalize(get_reference(), vcf).next()
self.assertEqual(record.samples[0].gt_nums, "1/2")
def testGenotypes(self):
# keep genotype info for a compound heterozygous call
vcf_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
chr1 2 . A C,T 20 PASS . GT 1/2\n
"""
vcf = self.getVcf(vcf_str)
record = normalize(get_reference(),vcf).next()
self.assertEqual(record.samples[0].gt_nums, "1/2")
def testChromEvaluateGenotypeConcordance(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
chr1 2 . A T 20 PASS . GT 0/1\n
chr1 5 . C T 20 PASS . GT 0/1\n
chr1 9 . A G 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
chr1 2 . A T 20 PASS . GT 1/1\n
chr1 6 . C G 20 PASS . GT 0/1\n
chr1 9 . A G 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr1')
pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HET][GENOTYPE_TYPE.HOM_VAR],1)
self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][GENOTYPE_TYPE.HOM_VAR],1)
# anything other than TP don't get counted in genotype concordance
self.assertEqual(cvs._nrd_counts(VARIANT_TYPE.SNP),(1,2))
# phased variants should be counted correctly
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
chr1 2 . A T 20 PASS . GT 0|1\n
chr1 9 . A G 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
chr1 2 . A T 20 PASS . GT 1|0\n
chr1 9 . A G 20 PASS . GT 1|1\n
"""
true_vars = vcf_to_ChromVariants(true_str,'chr1')
pred_vars = vcf_to_ChromVariants(pred_str,'chr1')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HET][GENOTYPE_TYPE.HET],1)
self.assertEqual(cvs.genotype_concordance[VARIANT_TYPE.SNP][GENOTYPE_TYPE.HOM_VAR][GENOTYPE_TYPE.HOM_VAR],1)
self.assertEqual(cvs._nrd_counts(VARIANT_TYPE.SNP),(0,2))
def testCleanOnly(self):
vcf_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
chr2 6 . g cg 20 PASS . GT 0/1\n
"""
norm = normalize(get_reference(), self.getVcf(vcf_str), 50, True)
record = norm.next()
self.assertEqual(record.POS, 6)
self.assertEqual(record.REF, 'G')
self.assertEqual(record.ALT, ['CG'])
def testCleanOnly(self):
vcf_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
chr2 6 . g cg 20 PASS . GT 0/1\n
"""
norm = normalize(get_reference(),self.getVcf(vcf_str),50,True)
record = norm.next()
self.assertEqual(record.POS,6)
self.assertEqual(record.REF,'G')
self.assertEqual(record.ALT,['CG'])
def testNormalizedToCollision(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr2 4 . C T 20 PASS . GT 0/1\n
chr2 5 . C CGC 20 PASS . GT 0/1\n
chr4 2 . A AGG 20 PASS . GT 0/1\n
chr4 6 . C CTC 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
r1 = norm_iter.next()
r2 = norm_iter.next()
r3 = norm_iter.next()
r4 = norm_iter.next()
self.assertEqual(r1.POS,4) # chr2 SNP doesn't change
self.assertEqual(r2.POS,5) # chr2 insertion gets normed forward 1 base and slid back to original pos
self.assertEqual(r2.REF,"C")
self.assertEqual(r2.ALT,["CGC"])
self.assertEqual(r3.POS,2)
self.assertEqual(r3.REF,"A")
self.assertEqual(r3.ALT,["AGG"])
self.assertEqual(r4.POS,3)
self.assertEqual(r4.REF,"T")
self.assertEqual(r4.ALT,["TCT"])
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 2 . ATC A 20 PASS . GT 0/1\n
chr4 6 . CTC C 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
r1 = norm_iter.next()
r2 = norm_iter.next()
self.assertEqual(r1.POS,2)
self.assertEqual(r1.REF,"ATC")
self.assertEqual(r1.ALT,["A"])
self.assertEqual(r2.POS,5)
self.assertEqual(r2.REF,"TCT")
self.assertEqual(r2.ALT,["T"])
def testMultipleAltAlleles(self):
# multiple alleles aren't normalized if the two alt alleles would be normalized differently
vcf_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
chr2 6 . G CG 20 PASS . GT 0/1\n
"""
record = normalize(get_reference(), self.getVcf(vcf_str)).next()
self.assertEqual(record.POS, 3)
self.assertEqual(record.REF, 'G')
self.assertEqual(record.ALT[0], 'GC')
vcf_str2 = """##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
chr2 6 . G CG,C 20 PASS . GT 0/1\n
"""
record = normalize(get_reference(), self.getVcf(vcf_str2)).next()
self.assertEqual(record.POS, 6)
self.assertEqual(record.REF, 'G')
self.assertEqual(record.ALT[0], 'CG')
def testMultipleAltAlleles(self):
# multiple alleles aren't normalized if the two alt alleles would be normalized differently
vcf_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
chr2 6 . G CG 20 PASS . GT 0/1\n
"""
record = normalize(get_reference(),self.getVcf(vcf_str)).next()
self.assertEqual(record.POS,3)
self.assertEqual(record.REF,'G')
self.assertEqual(record.ALT[0], 'GC')
vcf_str2 = """##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
chr2 6 . G CG,C 20 PASS . GT 0/1\n
"""
record = normalize(get_reference(),self.getVcf(vcf_str2)).next()
self.assertEqual(record.POS,6)
self.assertEqual(record.REF,'G')
self.assertEqual(record.ALT[0],'CG')
def testNormalizeTwoToCollision(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 4 . C CTC 20 PASS . GT 0/1\n
chr4 6 . C CTC 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(), self.getVcf(vcf_str))
r1 = norm_iter.next()
r2 = norm_iter.next()
self.assertEqual(r1.POS, 2)
self.assertEqual(r1.REF, "A")
self.assertEqual(r1.ALT, ["ATC"])
self.assertEqual(r2.POS, 3)
self.assertEqual(r2.REF, "T")
self.assertEqual(r2.ALT, ["TCT"])
def testNormalizeTwoToCollision(self):
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 4 . C CTC 20 PASS . GT 0/1\n
chr4 6 . C CTC 20 PASS . GT 0/1\n
"""
norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
r1 = norm_iter.next()
r2 = norm_iter.next()
self.assertEqual(r1.POS,2)
self.assertEqual(r1.REF,"A")
self.assertEqual(r1.ALT,["ATC"])
self.assertEqual(r2.POS,3)
self.assertEqual(r2.REF,"T")
self.assertEqual(r2.ALT,["TCT"])
def testIndelDeletionMismatchedAllele(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
chr3 5 . ATC A 20 PASS . GT 0/1\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 5 . ATCG A 20 PASS . GT 0/1
"""
true_vars = vcf_to_ChromVariants(true_str,'chr3')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr3')
cvs = chrom_evaluate_variants(true_vars,pred_vars,100,100,get_reference(),50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL],0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL],1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL],1)
def testVariantWithMismatchedRef(self):
fn_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
"""
fp_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 C 20 PASS . GT 1/1\n
chr2 4 . C T 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str, 'chr2')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr2')
rescuer = SequenceRescuer('chr2', 2, fn_vars, fp_vars,
get_empty_ChromVariants('chr2'),
get_reference(), 50)
self.assertFalse(rescuer.rescued)
def testNormalizedVariants(self):
fp_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 4 . C CTC 20 PASS . GT 0/1\n
chr4 6 . C CTC 20 PASS . GT 0/1\n
"""
fn_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 2 . A ATCTC 20 PASS . GT 0/1\n
"""
fp_vars = normalize_vcf_to_ChromVariants(fp_str, 'chr4')
fn_vars = vcf_to_ChromVariants(fn_str, 'chr4')
rescuer = SequenceRescuer('chr4', 2, fn_vars, fp_vars,
get_empty_ChromVariants('chr4'),
get_reference(), 50)
self.assertTrue(rescuer.rescued)
def testIndelDeletionMismatchedAllele(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
chr3 5 . ATC A 20 PASS . GT 0/1\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 5 . ATCG A 20 PASS . GT 0/1
"""
true_vars = vcf_to_ChromVariants(true_str, 'chr3')
pred_vars = vcf_to_ChromVariants(pred_str, 'chr3')
cvs = chrom_evaluate_variants(true_vars, pred_vars, 100, 100,
get_reference(), 50)
self.assertEqual(cvs.num_tp[VARIANT_TYPE.INDEL_DEL], 0)
self.assertEqual(cvs.num_fn[VARIANT_TYPE.INDEL_DEL], 1)
self.assertEqual(cvs.num_fp[VARIANT_TYPE.INDEL_DEL], 1)
def testEmptyWindow(self):
fn_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
chr1 8000 . G C 20 PASS . GT 1/1\n
"""
fp_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
chr1 10049 . CTTAAGCT C 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str, 'chr1')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr1')
rescuer = SequenceRescuer('chr1', 10049, fn_vars, fp_vars,
get_empty_ChromVariants('chr2'),
get_reference(), 50)
self.assertFalse(rescuer.rescued)
def test_approx_sv(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 269771 . 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)
self.truePositive(stat_reporter,VARIANT_TYPE.SV_INS)
self.trueNegative(stat_reporter,VARIANT_TYPE.SV_DEL)
def testNormalizeThreeCollision(self):
# the OP info flag is fake to force vars to right-slide
vcf_str = """##fileformat=VCFv4.0
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001\n
chr4 2 . A ATCTT 20 PASS OP=1 GT 0/1\n
chr4 2 . A T 20 PASS . GT 0/1\n
chr4 2 . ATCTC T 20 PASS OP=2 GT 0/1\n
"""
norm_iter = normalize(get_reference(),self.getVcf(vcf_str))
r1 = norm_iter.next()
r2 = norm_iter.next()
r3 = norm_iter.next()
r1,r2,r3 = sorted([r1,r2,r3],key=lambda x: x.POS) # order of vars from same pos not guaranteed
self.assertEqual(r1.POS,2)
self.assertEqual(r2.POS,3)
self.assertEqual(r2.REF,"T")
self.assertEqual(r2.ALT,["TCTTT"])
self.assertEqual(r3.POS,4)
self.assertEqual(r3.REF,"CTCTC")
self.assertEqual(r3.ALT,["C"])
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)
def testWindowTooBig(self):
longsv1 = 'ATTGTTCATGA' * 300
longsv2 = 'GCCTAGGGTCA' * 300
fn_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
chr1 7001 . """ + longsv1 + """ A 20 PASS . GT 1/1\n
chr1 10100 . """ + longsv2 + """ G 20 PASS . GT 0/1\n
"""
fp_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
chr1 10049 . CTTAAGCT C 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str, 'chr1')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr1')
rescuer = SequenceRescuer('chr1', 10049, fn_vars, fp_vars,
get_empty_ChromVariants('chr2'),
get_reference(), 50)
self.assertFalse(rescuer.rescued)
def testOverlappingVariants(self):
# if vcf contains overlapping variants, don't rescue that sequence
fn_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 1 . T G 20 PASS . GT 1/1\n
"""
tp_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 . GCC G 20 PASS . GT 1/1\n
chr2 4 . C G 20 PASS . GT 0/1\n
"""
fp_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 7 . GA A 20 PASS . GT 1/1\n
"""
tp_vars = vcf_to_ChromVariants(tp_str,'chr2')
fn_vars = vcf_to_ChromVariants(fn_str,'chr2')
fp_vars = vcf_to_ChromVariants(fp_str,'chr2')
rescuer = SequenceRescuer('chr2',1,fn_vars,fp_vars,tp_vars,get_reference(),50)
self.assertFalse(rescuer.rescued)
def testOverlappingVariants(self):
# if vcf contains overlapping variants, don't rescue that sequence
fn_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 1 . T G 20 PASS . GT 1/1\n
"""
tp_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 . GCC G 20 PASS . GT 1/1\n
chr2 4 . C G 20 PASS . GT 0/1\n
"""
fp_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 7 . GA A 20 PASS . GT 1/1\n
"""
tp_vars = vcf_to_ChromVariants(tp_str, 'chr2')
fn_vars = vcf_to_ChromVariants(fn_str, 'chr2')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr2')
rescuer = SequenceRescuer('chr2', 1, fn_vars, fp_vars, tp_vars,
get_reference(), 50)
self.assertFalse(rescuer.rescued)
def testNormalize(self):
#regular records are unchanged
vcf_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
chr1 2 . C A 20 PASS . GT 0/1\n
"""
norm_vcf = normalize(get_reference(),self.getVcf(vcf_str))
self.assertEqual(self.countRecords(norm_vcf),1)
#test that hom ref records are removed
vcf_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
chr1 2 . C C 20 PASS . GT 0/0\n
chr1 3 . G A 20 PASS . GT 1/1\n
"""
norm_vcf = normalize(get_reference(),self.getVcf(vcf_str))
self.assertEqual(self.countRecords(norm_vcf),1)
#test that SNP/indels without genotyping are removed
vcf_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
chr1 2 . C A 20 PASS . GT .\n
chr1 3 . G C 20 PASS . GT 0/0\n
chr1 4 . G T 20 PASS . GT 0|0\n
chr1 5 . G A 20 PASS . GT 1/1\n
"""
norm_vcf = normalize(get_reference(),self.getVcf(vcf_str))
self.assertEqual(self.countRecords(norm_vcf),1)
#test that SV without genotyping is retained
vcf_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
chr1 2 . C AAAAGAAAGGCATGACCTATCCACCCATGCCACCTGGATGGACCTCACAGGCACACTGCTTCATGAGAGAG 20 PASS . GT .\n
"""
norm_vcf = normalize(get_reference(),self.getVcf(vcf_str))
self.assertEqual(self.countRecords(norm_vcf),1)
#test that lower case ref/alt gets upper-cased
vcf_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
chr1 2 . c a 20 PASS . GT 0/1\n
"""
vcf_io = StringIO.StringIO(vcf_str)
lowercase_vcf = vcf.Reader(StringIO.StringIO(vcf_str))
output_vcf = normalize(get_reference(),self.getVcf(vcf_str))
original_r = lowercase_vcf.next()
norm_r = output_vcf.next()
self.assertEqual(original_r.REF,'c')
self.assertEqual(original_r.ALT[0], 'a')
self.assertEqual(norm_r.REF,'C')
self.assertEqual(norm_r.ALT[0],'A')
# test normalizing an insertion
vcf_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
chr1 9 . a ga 20 PASS . GT 0/1\n
"""
record = normalize(get_reference(),self.getVcf(vcf_str)).next()
self.assertEqual(record.POS,6)
self.assertEqual(record.REF,'C')
self.assertEqual(record.ALT,['CG'])
# test normalizing a deletion
vcf_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
chr1 5 . cc c 20 PASS . GT 0/1\n
"""
record = normalize(get_reference(),self.getVcf(vcf_str)).next()
self.assertEqual(record.POS,4)
self.assertEqual(record.REF,'GC')
self.assertEqual(record.ALT,['G'])
def testRescueMission(self):
# false negative variant at location is SV; don't rescue
fn_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
chr1 8000 . G GATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCT 20 PASS . GT 1/1\n
"""
fp_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
chr1 8000 . G GC 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(fn_str, 'chr1')
pred_vars = vcf_to_ChromVariants(fp_str, 'chr1')
num_new_tp, num_removed_fn = rescue_mission(
true_vars, pred_vars, get_empty_ChromVariants('chr1'), 8000,
get_reference(), 100)
self.assertFalse(any(map(lambda x: x > 0, num_new_tp.itervalues())))
self.assertFalse(any(map(lambda x: x > 0,
num_removed_fn.itervalues())))
# variant couldn't be rescued; no change to counts or ChromVariants
fn_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
chr1 2 . A C 20 PASS . GT 1/1\n
chr1 7 . C T 20 PASS . GT 0/1\n
"""
fp_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
chr1 4 . A C 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str, 'chr1')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr1')
num_new_tp, num_removed_fn = rescue_mission(
fn_vars, fp_vars, get_empty_ChromVariants('chr1'), 2,
get_reference(), 100)
self.assertFalse(any(map(lambda x: x > 0, num_new_tp.itervalues())))
self.assertFalse(any(map(lambda x: x > 0,
num_removed_fn.itervalues())))
self.assertEqual(len(fn_vars.all_locations), 2)
self.assertEqual(len(fp_vars.all_locations), 1)
# variant is rescued; counts change; variants are removed from fn/fp
fn_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
"""
fp_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
"""
fn_vars = vcf_to_ChromVariants(fn_str, 'chr2')
fp_vars = vcf_to_ChromVariants(fp_str, 'chr2')
num_new_tp, num_removed_fn = rescue_mission(
fn_vars, fp_vars, get_empty_ChromVariants('chr2'), 2,
get_reference(), 100)
self.assertEqual(num_new_tp[VARIANT_TYPE.INDEL_OTH], 1)
self.assertEqual(num_removed_fn[VARIANT_TYPE.SNP], 2)
self.assertEqual(len(fn_vars.all_locations), 0)
self.assertEqual(len(fp_vars.all_locations), 0)
def testRescueMission(self):
# false negative variant at location is SV; don't rescue
fn_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
chr1 8000 . G GATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCATTGCT 20 PASS . GT 1/1\n
"""
fp_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
chr1 8000 . G GC 20 PASS . GT 1/1\n
"""
true_vars = vcf_to_ChromVariants(fn_str,'chr1')
pred_vars = vcf_to_ChromVariants(fp_str,'chr1')
num_new_tp,num_removed_fn,rescuedvars = rescue_mission(true_vars,pred_vars,get_empty_ChromVariants('chr1'),8000,get_reference(),100)
self.assertFalse(any(map(lambda x: x > 0, num_new_tp.itervalues())))
self.assertFalse(any(map(lambda x: x > 0, num_removed_fn.itervalues())))
# variant couldn't be rescued; no change to counts or ChromVariants
fn_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
chr1 2 . A C 20 PASS . GT 1/1\n
chr1 7 . C T 20 PASS . GT 0/1\n
"""
fp_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
chr1 4 . A C 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr1')
fp_vars = vcf_to_ChromVariants(fp_str,'chr1')
num_new_tp,num_removed_fn,rescuedvars = rescue_mission(fn_vars,fp_vars,get_empty_ChromVariants('chr1'),2,get_reference(),100)
self.assertFalse(any(map(lambda x: x > 0, num_new_tp.itervalues())))
self.assertFalse(any(map(lambda x: x > 0, num_removed_fn.itervalues())))
self.assertEqual(len(fn_vars.all_locations),2)
self.assertEqual(len(fp_vars.all_locations),1)
self.assertEqual(rescuedvars,[])
# variant is rescued; counts change; variants are removed from fn/fp
fn_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
"""
fp_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
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr2')
fp_vars = vcf_to_ChromVariants(fp_str,'chr2')
num_new_tp,num_removed_fn,rescuedvars = rescue_mission(fn_vars,fp_vars,get_empty_ChromVariants('chr2'),2,get_reference(),100)
self.assertEqual(num_new_tp[VARIANT_TYPE.INDEL_OTH],1)
self.assertEqual(num_removed_fn[VARIANT_TYPE.SNP],2)
self.assertEqual(len(fn_vars.all_locations),0)
self.assertEqual(len(fp_vars.all_locations),0)
self.assertEqual(map(lambda r: r.pos,rescuedvars),[3,4])
def testTooManyPaths(self):
fn_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
chr1 10049 . CTTAAGCT C 20 PASS . GT 1/1\n
chr1 10053 . TGCGT T 20 PASS . GT 0/1\n
chr1 10055 . GCTAA G 20 PASS . GT 0/1\n
chr1 10057 . TA T 20 PASS . GT 1/1\n
chr1 10058 . GC G 20 PASS . GT 1/1\n
"""
fp_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
chr1 10025 . CTTAAGCT C 20 PASS . GT 1/1\n
chr1 10028 . TGCGT T 20 PASS . GT 0/1\n
chr1 10029 . GCTAA G 20 PASS . GT 0/1\n
chr1 10032 . TA T 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr1')
fp_vars = vcf_to_ChromVariants(fp_str,'chr1')
rescuer = SequenceRescuer('chr1',10000,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
self.assertFalse(rescuer.rescued)
def testEmptyWindow(self):
fn_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
chr1 8000 . G C 20 PASS . GT 1/1\n
"""
fp_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
chr1 10049 . CTTAAGCT C 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr1')
fp_vars = vcf_to_ChromVariants(fp_str,'chr1')
rescuer = SequenceRescuer('chr1',10049,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
self.assertFalse(rescuer.rescued)
def testWindowTooBig(self):
longsv1 = 'ATTGTTCATGA'*300
longsv2 = 'GCCTAGGGTCA'*300
fn_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
chr1 7001 . """ + longsv1 + """ A 20 PASS . GT 1/1\n
chr1 10100 . """ + longsv2 + """ G 20 PASS . GT 0/1\n
"""
fp_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
chr1 10049 . CTTAAGCT C 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr1')
fp_vars = vcf_to_ChromVariants(fp_str,'chr1')
rescuer = SequenceRescuer('chr1',10049,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
self.assertFalse(rescuer.rescued)
def testVariantWithMismatchedRef(self):
fn_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
"""
fp_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 C 20 PASS . GT 1/1\n
chr2 4 . C T 20 PASS . GT 1/1\n
"""
fn_vars = vcf_to_ChromVariants(fn_str,'chr2')
fp_vars = vcf_to_ChromVariants(fp_str,'chr2')
rescuer = SequenceRescuer('chr2',2,fn_vars,fp_vars,get_empty_ChromVariants('chr2'),get_reference(),50)
self.assertFalse(rescuer.rescued)
