def testGenotypes(self):
# normalize 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 20 PASS . GT 1/2\n
"""
vcf_io = StringIO.StringIO(vcf_str)
test_vcf = vcf.Reader(vcf_io)
output_io = StringIO.StringIO()
output_writer = VCFWriter(self.test_fasta, 'name', output_io)
normalize(self.test_fasta, test_vcf, output_writer)
output_vcf = self.outputToVcf(output_io)
record = output_vcf.next()
self.assertEqual(record.samples[0].gt_nums, "1/2")
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 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 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 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 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 normalize_vcf_to_ChromVariants(vcf_str,chrom):
str_io = StringIO.StringIO(vcf_str)
str_vcf = vcf.Reader(str_io)
norm_iter = normalize(get_reference(),str_vcf)
str_vars = Variants(norm_iter,MAX_INDEL_LEN)
return str_vars.on_chrom(chrom)
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 normalize_vcf_to_ChromVariants(vcf_str, chrom):
str_io = StringIO.StringIO(vcf_str)
str_vcf = vcf.Reader(str_io)
norm_iter = normalize(get_reference(), str_vcf)
str_vars = Variants(norm_iter, MAX_INDEL_LEN)
return str_vars.on_chrom(chrom)
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 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
"""
vcf_io = StringIO.StringIO(vcf_str)
norm_vcf = vcf.Reader(vcf_io)
output_io = StringIO.StringIO()
output_writer = VCFWriter(self.test_fasta, 'name', output_io)
normalize(self.test_fasta, norm_vcf, output_writer)
self.assertEqual(self.countRecords(self.outputToVcf(output_io)), 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
"""
vcf_io = StringIO.StringIO(vcf_str)
homref_vcf = vcf.Reader(vcf_io)
output_io = StringIO.StringIO()
output_writer = VCFWriter(self.test_fasta, 'name', output_io)
normalize(self.test_fasta, homref_vcf, output_writer)
self.assertEqual(self.countRecords(self.outputToVcf(output_io)), 0)
#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
"""
vcf_io = StringIO.StringIO(vcf_str)
homref_vcf = vcf.Reader(vcf_io)
output_io = StringIO.StringIO()
output_writer = VCFWriter(self.test_fasta, 'name', output_io)
normalize(self.test_fasta, homref_vcf, output_writer)
self.assertEqual(self.countRecords(self.outputToVcf(output_io)), 0)
#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
"""
vcf_io = StringIO.StringIO(vcf_str)
homref_vcf = vcf.Reader(vcf_io)
output_io = StringIO.StringIO()
output_writer = VCFWriter(self.test_fasta, 'name', output_io)
normalize(self.test_fasta, homref_vcf, output_writer)
self.assertEqual(self.countRecords(self.outputToVcf(output_io)), 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(vcf_io)
output_io = StringIO.StringIO()
output_writer = VCFWriter(self.test_fasta, 'name', output_io)
normalize(self.test_fasta, lowercase_vcf, output_writer)
output_vcf = self.outputToVcf(output_io)
lowercase_vcf = vcf.Reader(StringIO.StringIO(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')
