def test_illumina_writer(self):
# 01234
# 1234567890
# CCTGATTT-A
# TAACGA
# - C -A
vcf = '''##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER INFO
ref 1 . C T 10 PASS .
ref 2 . CT CA,C 10 PASS .
ref 3 . T A 10 PASS .
ref 4 . G C 10 PASS .
ref 5 . A G 10 PASS .
ref 6 . T A,C 10 PASS .
ref 7 . TT T 10 PASS .
ref 8 . T TA 10 PASS .
ref 10 . A C 10 PASS .
'''
vcf = vcf.replace(' ', '\t')
vcf_fhand = NamedTemporaryFile(suffix='.vcf')
vcf_fhand.write(vcf)
vcf_fhand.flush()
vcf_compressed = NamedTemporaryFile(suffix='.vcf.gz')
compress_with_bgzip(vcf_fhand, vcf_compressed)
index_vcf_with_tabix(vcf_compressed.name)
ref_fhand = NamedTemporaryFile(suffix='.fasta')
ref_fhand.write('>ref\nACTGATTTA\n')
ref_fhand.flush()
out_fhand1 = StringIO()
writer = IlluminaWriter(ref_fhand.name, out_fhand1, min_length=0,
vcf_fpath=vcf_compressed.name)
for snp in Reader(filename=vcf_compressed.name):
writer.write(snp)
# With no SNPs converted to IUPAC around
out_fhand2 = StringIO()
writer = IlluminaWriter(ref_fhand.name, out_fhand2, min_length=0)
for snp in Reader(filename=vcf_compressed.name):
writer.write(snp)
remove(vcf_compressed.name + '.tbi')
expected = u'CHROM\tPOS\tID\tseq\n'
expected += u'ref\t1\t.\t[C/T]*WSRHT-^A\n'
expected += u'ref\t2\t.\tY[CT/CA/C]SRHT-^A\n'
expected += u'ref\t3\t.\tYC[T/A]SRHT-^A\n'
expected += u'ref\t4\t.\tY*W[G/C]RHT-^A\n'
expected += u'ref\t5\t.\tY*WS[A/G]HT-^A\n'
expected += u'ref\t6\t.\tY*WSR[T/A/C]T-^A\n'
expected += u'ref\t7\t.\tY*WSRH[TT/T]A\n'
expected += u'ref\t8\t.\tY*WSRHT[T/TA]A\n'
expected += u'ref\t10\t.\tY*WSRHT-^A[A/C]\n'
assert expected == out_fhand1.getvalue()
expected = u'CHROM\tPOS\tID\tseq\nref\t1\t.\t[C/T]'
assert expected in out_fhand1.getvalue()
def test_errors(self):
# 01234
# 1234567890
# CCTGATTT-A
# TAACGA
# - C -A
vcf = '''##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER INFO
ref 1 . C T 10 PASS .
ref 2 . CT CA,C 10 PASS .
ref 3 . T A 10 PASS .
ref 4 . G C 10 PASS .
ref 5 . A G 10 PASS .
ref 6 . T A,C 10 PASS .
ref 7 . TT T 10 PASS .
ref 8 . T TA 10 PASS .
ref 10 . A C 10 PASS .
'''
vcf = vcf.replace(' ', '\t')
vcf_fhand = NamedTemporaryFile(suffix='.vcf')
vcf_fhand.write(vcf)
vcf_fhand.flush()
vcf_compressed = NamedTemporaryFile(suffix='.vcf.gz')
compress_with_bgzip(vcf_fhand, vcf_compressed)
index_vcf_with_tabix(vcf_compressed.name)
ref_fhand = NamedTemporaryFile(suffix='.fasta')
ref_fhand.write('>ref\nACTGATTTA\n')
ref_fhand.flush()
out_fhand = StringIO()
writer = IlluminaWriter(ref_fhand.name, out_fhand,
vcf_fpath=vcf_compressed.name)
snps = Reader(filename=vcf_compressed.name)
snp = snps.next()
try:
writer.write(snp)
self.fail('NotEnoughAdjacentSequenceError expected')
except IlluminaWriter.NotEnoughAdjacentSequenceError:
pass
def test_errors(self):
# 01234
# 1234567890
# CCTGATTT-A
# TAACGA
# - C -A
vcf = '''##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER INFO
ref 1 . C T 10 PASS .
ref 2 . CT CA,C 10 PASS .
ref 3 . T A 10 PASS .
ref 4 . G C 10 PASS .
ref 5 . A G 10 PASS .
ref 6 . T A,C 10 PASS .
ref 7 . TT T 10 PASS .
ref 8 . T TA 10 PASS .
ref 10 . A C 10 PASS .
'''
vcf = vcf.replace(' ', '\t')
vcf_fhand = NamedTemporaryFile(suffix='.vcf')
vcf_fhand.write(vcf)
vcf_fhand.flush()
vcf_compressed = NamedTemporaryFile(suffix='.vcf.gz')
compress_with_bgzip(vcf_fhand, vcf_compressed)
index_vcf_with_tabix(vcf_compressed.name)
ref_fhand = NamedTemporaryFile(suffix='.fasta')
ref_fhand.write('>ref\nACTGATTTA\n')
ref_fhand.flush()
out_fhand = StringIO()
writer = IlluminaWriter(ref_fhand.name, out_fhand,
vcf_fpath=vcf_compressed.name)
snps = Reader(filename=vcf_compressed.name)
snp = snps.next()
try:
writer.write(snp)
self.fail('NotEnoughAdjacentSequenceError expected')
except IlluminaWriter.NotEnoughAdjacentSequenceError:
pass
def test_illumina_writer(self):
# 01234
# 1234567890
# CCTGATTT-A
# TAACGA
# - C -A
vcf = '''##fileformat=VCFv4.1
#CHROM POS ID REF ALT QUAL FILTER INFO
ref 1 . C T 10 PASS .
ref 2 . CT CA,C 10 PASS .
ref 3 . T A 10 PASS .
ref 4 . G C 10 PASS .
ref 5 . A G 10 PASS .
ref 6 . T A,C 10 PASS .
ref 7 . TT T 10 PASS .
ref 8 . T TA 10 PASS .
ref 10 . A C 10 PASS .
'''
vcf = vcf.replace(' ', '\t')
vcf_fhand = NamedTemporaryFile(suffix='.vcf')
vcf_fhand.write(vcf)
vcf_fhand.flush()
vcf_compressed = NamedTemporaryFile(suffix='.vcf.gz')
compress_with_bgzip(vcf_fhand, vcf_compressed)
index_vcf_with_tabix(vcf_compressed.name)
ref_fhand = NamedTemporaryFile(suffix='.fasta')
ref_fhand.write('>ref\nACTGATTTA\n')
ref_fhand.flush()
out_fhand1 = StringIO()
writer = IlluminaWriter(ref_fhand.name, out_fhand1, min_length=0,
vcf_fpath=vcf_compressed.name)
for snp in Reader(filename=vcf_compressed.name):
writer.write(snp)
# With no SNPs converted to IUPAC around
out_fhand2 = StringIO()
writer = IlluminaWriter(ref_fhand.name, out_fhand2, min_length=0)
for snp in Reader(filename=vcf_compressed.name):
writer.write(snp)
remove(vcf_compressed.name + '.tbi')
expected = u'CHROM\tPOS\tID\tseq\n'
expected += u'ref\t1\t.\t[C/T]*WSRHT-^A\n'
expected += u'ref\t2\t.\tY[CT/CA/C]SRHT-^A\n'
expected += u'ref\t3\t.\tYC[T/A]SRHT-^A\n'
expected += u'ref\t4\t.\tY*W[G/C]RHT-^A\n'
expected += u'ref\t5\t.\tY*WS[A/G]HT-^A\n'
expected += u'ref\t6\t.\tY*WSR[T/A/C]T-^A\n'
expected += u'ref\t7\t.\tY*WSRH[TT/T]A\n'
expected += u'ref\t8\t.\tY*WSRHT[T/TA]A\n'
expected += u'ref\t10\t.\tY*WSRHT-^A[A/C]\n'
assert expected == out_fhand1.getvalue()
expected = u'CHROM\tPOS\tID\tseq\nref\t1\t.\t[C/T]'
assert expected in out_fhand1.getvalue()