def test_sameGenomicPosition(self):
v = variant(chromosome=3, start=6)
w = variant(chromosome=3, start=6)
self.assertTrue(v.sameGenomicPosition(w))
w.chromosome = 4
self.assertFalse(v.sameGenomicPosition(w))
w.start = 9
self.assertFalse(v.sameGenomicPosition(w))
w.chromosome = 3
w.start = 9
self.assertFalse(v.sameGenomicPosition(w))
def test_empty_init(self):
v = variant()
self.assertTrue(v.gene == "")
self.assertTrue(v.chromosome == None)
self.assertTrue(v.start == None)
self.assertTrue(v.stop == None)
self.assertTrue(v.reference == "-")
self.assertTrue(v.alternate == "-")
self.assertTrue(v.strand == "+")
self.assertTrue(v.sample == None)
self.assertTrue(v.assembly == None)
self.assertTrue(v.dbsnp == None)
def main( argv ):
values = parseArgs( argv )
inputFile = values["input"]
outputFile = values["output"]
genVar = values["genVar"]
tsv = values["tsv"]
results = ""
exacInstance = exacapi()
print genVar
g = genVar.split( '-' )
var = variant.variant( chromosome=g[0] , start=g[1] , reference=g[2] , mutant=g[3] )
var.reference = 'd'
aF = exacInstance.getAlleleFrequency( var )
var.printVariant(' ')
print "Allele Frequency = " + str(aF)
def searchVCF(self, **kwargs):
vcf = kwargs.get('vcf', "")
self.variants = kwargs.get('queries', [])
entries = {}
with pysam.VariantFile(vcf, "r") as vf:
for var in self.variants:
here = str(var.chromosome) + ':' + str(var.start) + '-' + str(
var.stop)
for hit in vf.fetch(region=here):
for i in range(0, len(hit.alts)):
evar = variant( chromosome = hit.contig , \
start = hit.start + 1 , \
dbsnp = hit.id , \
reference = hit.alleles[0] , \
alternate = hit.alts[i] , \
)
if var.sameGenomicVariant(evar):
entries[var.genomicVar()] = hit.info["AF"][i]
return entries
def main(argv):
values = parseArgs(argv)
inputFile = values["input"]
outputFile = values["output"]
genVar = values["genVar"]
tsv = values["tsv"]
results = ""
exacInstance = exacapi()
print genVar
g = genVar.split('-')
var = variant.variant(chromosome=g[0],
start=g[1],
reference=g[2],
mutant=g[3])
var.reference = 'd'
aF = exacInstance.getAlleleFrequency(var)
var.printVariant(' ')
print "Allele Frequency = " + str(aF)
def test_empty_init(self):
v = variant()
self.assertFalse(v)