def testUnknown(self):
self.logger.info("BEGIN")
# TRUE GAT
# pos 123
ref = "r1 GAT"
s1 = "s1 -*-"
s2 = "s2 **-"
s3 = "s3 ***"
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
msasList1 = msa2vcf._parseMSASample(offset, ref, s1)
self.logger.info("msasList1:\n{}".format(msasList1))
self.assertEqual(msasList1, [])
msasList2 = msa2vcf._parseMSASample(offset, ref, s3)
self.logger.info("msasList2:\n{}".format(msasList2))
self.assertEqual(msasList2, [])
msasList3 = msa2vcf._parseMSASample(offset, ref, s3)
self.logger.info("msasList3:\n{}".format(msasList3))
self.assertEqual(msasList3, [])
vcfList, sampleNamesList = msa2vcf._parseMSASampleList(
offset, ref, [s1, s2, s3])
self.assertEqual(vcfList, [])
self.logger.info("END\n")
def testInsert(self):
self.logger.info("BEGIN")
# TRUE G C
# pos 1 2
ref = " r G.C"
s1 = "s1 -A-"
s2 = "s2 -A-"
s3 = "s3 -G-"
expected = [
"r 1 . G GA . PASS . GT 1 1 0",
"r 1 . G GG . PASS . GT 0 0 1",
]
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
vcfList, sampleNameList = msa2vcf._parseMSASampleList(
offset, ref, [s1, s2, s3])
for i in range(len(vcfList)):
vcf = vcfList[i]
self.logger.info("i:{} vcf:{}".format(i, vcf))
e = str(expected[i])
self.logger.info(" e:{}\n".format(e))
# cleanE = "".join(e.split()) # remove whitespace
self.logger.info("AEDWIP:{}".format(str(vcf).split()))
cleanV = " ".join(str(vcf).split())
self.logger.info("cleanV:{}".format(cleanV))
self.logger.info("cleanE:{}".format(e))
self.assertEqual(cleanV, e)
self.logger.info("END\n")
def testDeleteRun(self):
self.logger.info("BEGIN")
# true GATT
# pos 1234
ref = "ref GATT"
s1 = "s1 -..-" # middle
s2 = "s1 -..." # end
s3 = "s1 ...-" # beginning
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
msaList = msa2vcf._parseMSASample(offset, ref, s1)
self.logger.info("msaList:\n{}".format(msaList))
e1 = "CHROM:ref sample:s1 POS:1 ID:. REF:GAT ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(msaList[0]), e1)
msaList = msa2vcf._parseMSASample(offset, ref, s2)
self.logger.info("msaList:\n{}".format(msaList))
e2 = "CHROM:ref sample:s1 POS:1 ID:. REF:GATT ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(msaList[0]), e2)
msaList = msa2vcf._parseMSASample(offset, ref, s3)
self.logger.info("msaList:\n{}".format(msaList))
e3 = "CHROM:ref sample:s1 POS:1 ID:. REF:GATT ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(msaList[0]), e3)
self.logger.info("END\n")
def testParsemsaSampleList(self):
self.logger.info("BEGIN")
ref = "r1 GAT"
s1 = "s1 -T-"
s2 = "s2 -C-"
s3 = "s3 -T-"
s4 = "s4 -.-"
s5 = "s5 -.-"
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
vcfList, sampleNamesList = msa2vcf._parseMSASampleList(
offset, ref, [s1, s2, s3, s4, s5])
expected = [
"r1 1 . GA G . PASS . GT 0 0 0 1 1",
"r1 2 . A T . PASS . GT 1 0 1 0 0",
"r1 2 . A C . PASS . GT 0 1 0 0 0",
]
for i in range(len(vcfList)):
vcf = vcfList[i]
self.logger.info("i:{} vcf:{}".format(i, vcf))
self.logger.info(" e:{}\n".format(expected[i]))
e = expected[i]
cleanE = "".join(e.split()) # remove whitespace
cleanV = "".join(str(vcf).split())
self.assertEqual(cleanV, cleanE, " i:{}".format(i))
self.logger.info("END\n")
def testBug287(self):
"""
E_gen.txt
error:[vg::Constructor] Variant/reference sequence mismatch: A vs pos: 287: C; do your VCF and FASTA coordinates match?
Variant: E*01:01:01:01 287 . A AA 0 PASS .
zero ind: 286 1-indexed: 287
"""
self.logger.info("BEGIN")
ref1 = "ref A.G"
s1 = "s1 ***"
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
msaList1 = msa2vcf._parseMSASample(offset, ref1, s1)
self.logger.info("msalist1:\n{}".format(msaList1))
self.assertEqual(msaList1, [])
# true AGCA G
#pos 1234 5
ref2 = "ref2 AGCA.G"
s2 = "s2 **--C-"
msaList2 = msa2vcf._parseMSASample(offset, ref2, s2)
self.logger.info("msalist2:\n{}".format(msaList2))
e2 = "CHROM:ref2 sample:s2 POS:4 ID:. REF:A ALT:AC QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.insertion"
self.assertEqual(str(msaList2[0]), e2)
self.logger.info("END\n")
def testParseMSASample_GoodSNP(self):
self.logger.info("BEGIN")
# data/A_gen.txt
# snp at beginning
ref = "A*01:01:01:01 CAGGAGCAGA GGGGTCAGGG ATTGGGGAGT CCCAGCCTTG "
seq1 = "A*01:01:01:02 T--------- ---------- ---------- ---------- "
# CHROM:A*01:01:01:01 sample:A*01:01:01:02 POS:1 ID:. REF:C ALT:T QUAL. FILTER:PASS INFO: FORMAT:GT VariantType.polymorphism
# snp in middle
seq2 = "A*01:01:01:03 -----C---- ---------- ---------- ---------- "
# result2:A*01:01:01:03 6 . G C . PASS .
# "CHROM:A*01:01:01:01 sample:A*01:01:01:03 POS:6 ID:. REF:G ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
# snp at end of block
seq3 = "A*01:01:01:04 ---------C ---------- ---------- ---------- "
# result3:A*01:01:01:04 10 . A C . PASS .
# CHROM:A*01:01:01:01 sample:A*01:01:01:04 POS:10 ID:. REF:A ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism
# multiple snps
seq4 = "A*01:01:01:05 ---------C ---------- -AA------- ---------- "
# A*01:01:01:05 10 . A C . PASS .
# "CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:10 ID:. REF:A ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism",
# A*01:01:01:05 22 . T A . PASS
#"CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:22 ID:. REF:T ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism",
# A*01:01:01:05 23 . T A . PASS .
# "CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:23 ID:. REF:T ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
result1List = msa2vcf._parseMSASample(offset, ref, seq1)
self.logger.info("result1[0]:\n{}\t".format(result1List[0]))
r1Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:02 POS:1 ID:. REF:C ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(result1List[0]), r1Expected)
result2List = msa2vcf._parseMSASample(offset, ref, seq2)
self.logger.info("result2[0]:\n{}".format(result2List[0]))
r2Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:03 POS:6 ID:. REF:G ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(result2List[0]), r2Expected)
result3List = msa2vcf._parseMSASample(offset, ref, seq3)
self.logger.info("result3[0]:\n{}".format(result3List[0]))
r3Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:04 POS:10 ID:. REF:A ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(result3List[0]), r3Expected)
result4List = msa2vcf._parseMSASample(offset, ref, seq4)
r4Expected = [
"CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:10 ID:. REF:A ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism",
"CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:22 ID:. REF:T ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism",
"CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:23 ID:. REF:T ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
]
for i in range(len(result4List)):
msas = result4List[i]
self.logger.info("msas{}:\n{}".format(i, msas))
self.assertEqual(str(msas), r4Expected[i])
self.logger.info("END\n")
def testCreateAbstractSyntaxTree(self):
self.logger.info("BEGIN")
ref = "r1 GAT"
s1 = "s1 -T-"
s2 = "s2 -C-"
s3 = "s3 -T-"
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
msasList1 = msa2vcf._parseMSASample(offset, ref, s1)
msasList2 = msa2vcf._parseMSASample(offset, ref, s2)
msasList3 = msa2vcf._parseMSASample(offset, ref, s3)
msasList = msasList1 + msasList3 + msasList2 # test sampleNamesList is sorted correctly
for msas in msasList:
self.logger.info("msas:{}".format(msas))
sampleNamesList, sampleNameLookUp, AST = msa2vcf._createAbstractSyntaxTree(
msasList)
self.logger.info("sampleNamesList:{}".format(sampleNamesList))
self.assertEqual(sampleNamesList, ['s1', 's2', 's3'])
self.logger.info("sampleNameLookUp:{}".format(sampleNameLookUp))
self.assertEqual(sampleNameLookUp, {'s1': 0, 's2': 1, 's3': 2})
self.logger.info("ast:{}".format(AST))
pp = pprint.PrettyPrinter()
#pp.pprint(AST) # debug line comment this line out mess up unit test summary output
ASTStr = pp.pformat(AST)
deletionVCF = AST['r1POS:2'][MSAVCF.VariantType.deletion]
self.logger.info("deletionVCF:\n{}".format(deletionVCF))
self.assertEqual(deletionVCF, {})
insertionsVCF = AST['r1POS:2'][MSAVCF.VariantType.insertion]
self.logger.info("insertionsVCF:\n{}".format(insertionsVCF))
self.assertEqual(insertionsVCF, {})
unknownVCF = AST['r1POS:2'][MSAVCF.VariantType.unknown]
self.logger.info("unknownVCF:\n{}".format(unknownVCF))
self.assertEqual(unknownVCF, {})
polymorphismVCF = AST['r1POS:2'][MSAVCF.VariantType.polymorphism]
self.logger.info("polymorphismVCF:\n{}".format(polymorphismVCF))
expectedP = "{'T': [CHROM:r1 sample:s1 POS:2 ID:. REF:A ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism, CHROM:r1 sample:s3 POS:2 ID:. REF:A ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism], 'C': [CHROM:r1 sample:s2 POS:2 ID:. REF:A ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism]}"
self.assertEqual(str(polymorphismVCF), expectedP)
self.logger.info("END\n")
def testTricky2(self):
self.logger.info("BEGIN")
# true GA CT
# ps 12 34
ref1 = "r1 GA|CT"
s1 = "s1 ---A-"
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
msaList1 = msa2vcf._parseMSASample(offset, ref1, s1)
self.logger.info("msalist1:\n{}".format(msaList1))
e1 = "CHROM:r1 sample:s1 POS:3 ID:. REF:C ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList1[0]), e1)
self.logger.info("END\n")
def testInsertRunAtEND(self):
self.logger.info("BEGIN")
# TRUE GATTA
# POS 12345
ref3 = "ref1 GATT.."
s3 = "s3 ----AC"
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
msaList = msa2vcf._parseMSASample(offset, ref3, s3)
self.logger.info("msaList:\n{}".format(msaList))
# TODO: check with Jonas is position correct?
e3 = "CHROM:ref1 sample:s3 POS:4 ID:. REF:T ALT:TAC QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.insertion"
self.assertEqual(str(msaList[0]), e3)
self.logger.info("END")
def testTricky(self):
self.logger.info("BEGIN")
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
# true GAATT
# pos 12345
ref1 = "ref1 GAATT"
s1 = "s1 **--C"
msaList = msa2vcf._parseMSASample(offset, ref1, s1)
self.logger.info("msaList:\n{}".format(msaList))
e1 = "CHROM:ref1 sample:s1 POS:5 ID:. REF:T ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[0]), e1)
# true GAATT GA
# pos 12345 67
ref2 = "ref2 GAATT.GA"
s2 = "s2 **--C.-C"
msaList = msa2vcf._parseMSASample(offset, ref2, s2)
self.logger.info("msaList:\n{}\n".format(msaList))
e2 = "CHROM:ref2 sample:s2 POS:5 ID:. REF:T ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[0]), e2)
e3 = "CHROM:ref2 sample:s2 POS:7 ID:. REF:A ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[1]), e3)
# true GAATT GA G
# pos 12345 67 8
ref4 = "ref4 GAATT.GA*G"
s4 = "s4 **--C.-CAT"
msaList = msa2vcf._parseMSASample(offset, ref4, s4)
self.logger.info("msaList:\n{}\n".format(msaList))
e4 = "CHROM:ref4 sample:s4 POS:5 ID:. REF:T ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[0]), e4)
e5 = "CHROM:ref4 sample:s4 POS:7 ID:. REF:A ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[1]), e5)
e6 = "CHROM:ref4 sample:s4 POS:8 ID:. REF:G ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[2]), e6)
self.logger.info("END\n")
def testDeleteRunAtEnd(self):
self.logger.info("BEGIN")
self.logger.info("BEGIN")
# true CAGGAGCAGA
# pos 1234567890
ref = "ref CAGGAGCAGA"
seq1 = "s1 -------..."
# result1:A*01:01:01:02 1 . C . . PASS .
# CHROM:ref sample:seq1 POS:7 ID:. REF:CAGA ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
msaList = msa2vcf._parseMSASample(offset, ref, seq1)
self.logger.info("msaList:\n{}".format(msaList))
e1 = "CHROM:ref sample:s1 POS:7 ID:. REF:CAGA ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(msaList[0]), e1)
self.logger.info("END\n")
def testAGenBug288(self):
"""
A_gen.txt. bug at position 288 in sample A*68:02:01:0
"""
self.logger.info("BEGIN")
# true CCC AGACGCCGAGG
# pos 123 45678901234
ref1 = "r1 CCC.AGACGCCGAGG"
s1 = "s1 --............-"
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
msaList1 = msa2vcf._parseMSASample(offset, ref1, s1)
self.logger.info("msaList1:\n{}".format(msaList1))
e1 = "CHROM:r1 sample:s1 POS:2 ID:. REF:CCAGACGCCGAG ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(msaList1[0]), e1)
self.logger.info("END\n")
def testVGConstructBug(self):
"""
index file shortenBug2299_1,2180d.out.fasta.fai not found, generating...
error:[vg::Constructor] Variant/reference sequence mismatch: TC vs pos: 111: CC; do your VCF and FASTA coordinates match?
Variant: ref 111 . TC T 0 PASS .
zero ind: 110 1-indexed: 111
"""
self.logger.info("BEGIN")
# true A GTCCCC
# pos 1 234567
ref1 = "ref A|GTCCCC"
s1 = "s1 -|--.---"
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
msaList1 = msa2vcf._parseMSASample(offset, ref1, s1)
self.logger.info("msalist1:\n{}".format(msaList1))
e1 = "CHROM:ref sample:s1 POS:3 ID:. REF:TC ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(msaList1[0]), e1)
self.logger.info("END\n")
def testParseMSASample_DeleteEndSNP(self):
self.logger.info("BEGIN")
# data/A_gen.txt
# SNP delete at end
#true CAGGAGCAGA
#pos 1234567890
ref = "A*01:01:01:01 CAGGAGCAGA"
seq1 = "A*01:01:01:04 ---------."
# result3:A*01:01:01:04 10 . GA G . PASS .
# CHROM:A*01:01:01:01 sample:A*01:01:01:04 POS:9 ID:. REF:GA ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
result1List = msa2vcf._parseMSASample(offset, ref, seq1)
self.logger.info("result1[0]:\n{}".format(result1List[0]))
r1Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:04 POS:9 ID:. REF:GA ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(result1List[0]), r1Expected)
self.logger.info("END\n")
def testInsertAtBegining(self):
self.logger.info("BEGIN")
# TRUE A
# POS 1234
ref = "ref1 ....ACTA"
s1 = "s1 GATT---G"
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
msaList = msa2vcf._parseMSASample(offset, ref, s1)
for msa in msaList:
self.logger.info("msa:\n{}".format(msa))
# TODO: check with Jonas is position correct?
e1 = "CHROM:ref1 sample:s1 POS:1 ID:. REF:A ALT:GATTA QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.insertion"
self.assertEqual(str(msaList[0]), e1)
e2 = "CHROM:ref1 sample:s1 POS:4 ID:. REF:A ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[1]), e2)
self.logger.info("END")
def testDeleteRunAtBegining(self):
self.logger.info("BEGIN")
# true CAG
# pos 1234567890
ref = "ref CAGGAGCAGA"
seq1 = "s1 ...------T"
# result1:A*01:01:01:02 1 . C . . PASS .
# CHROM:A*01:01:01:01 sample:A*01:01:01:02 POS:7 ID:. REF:CAGA ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
msaList = msa2vcf._parseMSASample(offset, ref, seq1)
for msa in msaList:
self.logger.info("msa:{}".format(msa))
self.logger.info("msaList:\n{}".format(msaList))
e1 = "CHROM:ref sample:s1 POS:1 ID:. REF:CAGG ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(msaList[0]), e1)
e2 = "CHROM:ref sample:s1 POS:10 ID:. REF:A ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList[1]), e2)
self.logger.info("END\n")
def testTemplate3579(self):
"""
+ ../vg/bin/vg construct -r shortenBug3579_1,0d.out.fasta -v shortenBug3579_1,0d.out.vcf.gz
index file shortenBug3579_1,0d.out.fasta.fai not found, generating...
error:[vg::Constructor] Variant/reference sequence mismatch: C vs pos: 724: T; do your VCF and FASTA coordinates match?
Variant: ref 724 . C T 0 PASS .
"""
self.logger.info("BEGIN")
# test cased based on file E*01:01:01:01.sequence.w100-E*01:03:02:07.sequence.w100
#true AACC GG TT AC GTC
#pos 1234 56 78 90 123
ref1 = "r1 AACC.GG|TT|AC|GTC"
s1 = "s1 **--.--|--|--|--T"
offset = 0
msa2vcf = MSAVCF.MSA2VCFImplementation()
msaList1 = msa2vcf._parseMSASample(offset, ref1, s1)
self.logger.info("msaList1:\n{}".format(msaList1))
e1 = "CHROM:r1 sample:s1 POS:13 ID:. REF:C ALT:T QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.assertEqual(str(msaList1[0]), e1)
self.logger.info("END\n")
def testInsertRun(self):
self.logger.info("BEGIN")
# TRUE G T
# pos 1 2
ref1 = "ref1 G..T"
s1 = "s1 -AT-"
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
msaList = msa2vcf._parseMSASample(offset, ref1, s1)
self.logger.info("msaList:\n{}".format(msaList))
e1 = "CHROM:ref1 sample:s1 POS:1 ID:. REF:G ALT:GAT QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.insertion"
self.assertEqual(str(msaList[0]), e1)
# TRUE G
# pos 1
ref2 = "ref1 G..."
s2 = "s2 -ATT"
msaList = msa2vcf._parseMSASample(offset, ref2, s2)
self.logger.info("msaList:\n{}".format(msaList))
e2 = "CHROM:ref1 sample:s2 POS:1 ID:. REF:G ALT:GATT QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.insertion"
self.assertEqual(str(msaList[0]), e2)
# TRUE G T
# POS 1 2
ref4 = "ref1 G..T"
s4 = "s4 -ATC"
msaList = msa2vcf._parseMSASample(offset, ref4, s4)
e4a = "CHROM:ref1 sample:s4 POS:1 ID:. REF:G ALT:GAT QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.insertion"
e4b = "CHROM:ref1 sample:s4 POS:2 ID:. REF:T ALT:C QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.polymorphism"
self.logger.info("msaList:\n{}".format(msaList))
self.assertEqual(str(msaList[0]), e4a)
self.assertEqual(str(msaList[1]), e4b)
def testParseMSASample_DeleteSNP(self):
self.logger.info("BEGIN")
# data/A_gen.txt
# SNP delete at beginning
# true CAG
# pos 123
ref = "A*01:01:01:01 CAGGAGCAGA GGGGTCAGGG ATTGGGGAGT CCCAGCCTTG "
seq1 = "A*01:01:01:02 .--------- ---------- ---------- ---------- "
# result1:A*01:01:01:02 1 . C . . PASS .
# CHROM:A*01:01:01:01 sample:A*01:01:01:02 POS:1 ID:. REF:C ALT:. QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion
# SNP delete at middle of block
#true CAGGAGCAGA
#pos 1234567890
seq2 = "A*01:01:01:03 -----.---- ---------- ---------- ---------- "
# result2:A*01:01:01:03 6 . AG A . PASS .
# CHROM:A*01:01:01:01 sample:A*01:01:01:03 POS:5 ID:. REF:AG ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion
# SNP delete at end of block
#true CAGGAGCAGA
#pos 1234567890
seq3 = "A*01:01:01:04 ---------. ---------- ---------- ---------- "
# result3:A*01:01:01:04 10 . GA G . PASS .
# CHROM:A*01:01:01:01 sample:A*01:01:01:04 POS:9 ID:. REF:GA ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion
#true CAGGAGCAGA GGGGTCAGGG
#pos 1234567890 1234567890
seq4 = "A*01:01:01:05 ---------- .--------- ---------- ---------- "
# result4:A*01:01:01:05 11 . AG A . PASS .
# CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:10 ID:. REF:AG ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion
# multiple SNP deletes
#true CAGGAGCAGA GGGGTCAGGG ATTGGGGAGT
#pos 1234567890 1234567890 1234567890
seq5 = "A*01:01:01:06 ---------. ---------- -..------- ---------- "
# A*01:01:01:06 9 . GA G . PASS .
# A*01:01:01:06 21 . ATT A . PASS .
msa2vcf = MSAVCF.MSA2VCFImplementation()
offset = 0
result1List = msa2vcf._parseMSASample(offset, ref, seq1)
self.logger.info("result1[0]:\n{}".format(result1List[0]))
r1Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:02 POS:1 ID:. REF:CA ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(result1List[0]), r1Expected)
result2List = msa2vcf._parseMSASample(offset, ref, seq2)
self.logger.info("result2[0]:\n{}".format(result2List[0]))
r2Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:03 POS:5 ID:. REF:AG ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(result2List[0]), r2Expected)
result3List = msa2vcf._parseMSASample(offset, ref, seq3)
self.logger.info("result3[0]:\n{}".format(result3List[0]))
r3Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:04 POS:9 ID:. REF:GA ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(result3List[0]), r3Expected)
result4List = msa2vcf._parseMSASample(offset, ref, seq4)
self.logger.info("result4[0]:\n{}".format(result4List[0]))
r4Expected = "CHROM:A*01:01:01:01 sample:A*01:01:01:05 POS:10 ID:. REF:AG ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion"
self.assertEqual(str(result4List[0]), r4Expected)
result5List = msa2vcf._parseMSASample(offset, ref, seq5)
r5Expected = [
"CHROM:A*01:01:01:01 sample:A*01:01:01:06 POS:9 ID:. REF:GA ALT:G QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion",
"CHROM:A*01:01:01:01 sample:A*01:01:01:06 POS:21 ID:. REF:ATT ALT:A QUAL. FILTER:PASS INFO:. FORMAT:GT VariantType.deletion",
]
for i in range(len(result5List)):
msas = result5List[i]
self.logger.info("\nmsas:{}:{}".format(i, msas))
self.assertEqual(str(msas), r5Expected[i])
self.logger.info("END\n")