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)