def setUp(self):
self.solution ={'A':allele("A"),
'T':allele("T"),
'C':allele("C"),
'G':allele("G"),
'-':allele("-")}
self.solution["A"].count = 11
self.solution["A"].freq = 11/18.0
self.solution["T"].count = 4
self.solution["T"].freq = 4/18.0
self.solution["C"].count = 1
self.solution["C"].freq = 1/18.0
self.solution["G"].count = 1
self.solution["G"].freq = 1/18.0
self.solution["-"].count = 1
self.solution["-"].freq = 1/18.0
self.pileup = "AAAAATTAATTAAA-AGC"
self.l = locus(pos =0)
for b in self.pileup:
self.l.update(b)
def test_outside_splice(self):
output = {
"ORF": "myFavoriteProtien",
"codonPos": None,
"codingPos": None,
"aminoAcidPos": None,
"consensusAA": None,
"varAA": None,
"classification": "Noncoding"
}
a = allele("T")
a.classifyVar(self.sequence, self.codingRegion[0], 1)
self.assertEqual(output, a.mutationalClass[0])
def test_stop(self):
output = {
"ORF": "myFavoriteProtien_alternate_splice",
"codonPos": 0,
"codingPos": 3,
"aminoAcidPos": 1,
"consensusAA": "E",
"varAA": "*",
"classification": "Stop"
}
a = allele("T")
a.classifyVar(self.sequence, self.codingRegion[1], 6)
self.assertEqual(output, a.mutationalClass[0])
def test_readthrough(self):
output = {
"ORF": "myFavoriteProtien",
"codonPos": 0,
"codingPos": 15,
"aminoAcidPos": 5,
"consensusAA": "*",
"varAA": "E",
"classification": "Readthrough"
}
a = allele("G")
a.classifyVar(self.sequence, self.codingRegion[0], 25)
self.assertEqual(output, a.mutationalClass[0])
def test_S(self):
output = {
"ORF": "myFavoriteProtien",
"codonPos": 2,
"codingPos": 14,
"aminoAcidPos": 4,
"consensusAA": "E",
"varAA": "E",
"classification": "Synonymous"
}
a = allele("G")
a.classifyVar(self.sequence, self.codingRegion[0], 24)
self.assertEqual(output, a.mutationalClass[0])
def test_NS(self):
output = {
"ORF": "myFavoriteProtien",
"codonPos": 0,
"codingPos": 3,
"aminoAcidPos": 1,
"consensusAA": "A",
"varAA": "P",
"classification": "Nonsynonymous"
}
a = allele("C")
a.classifyVar(self.sequence, self.codingRegion[0], 6)
self.assertEqual(output, a.mutationalClass[0])
def test_indel(self):
output = {
"ORF": "myFavoriteProtien",
"codonPos": 1,
"codingPos": 1,
"aminoAcidPos": 0,
"consensusAA": "M",
"varAA": None,
"classification": "Indel"
}
a = allele("-")
a.classifyVar(self.sequence, self.codingRegion[0], 4)
self.assertEqual(output, a.mutationalClass[0])
def setUp(self):
self.solution = {
'A': allele("A"),
'T': allele("T"),
'C': allele("C"),
'G': allele("G"),
'-': allele("-")
}
self.solution["A"].count = 11
self.solution["A"].freq = 11 / 18.0
self.solution["T"].count = 4
self.solution["T"].freq = 4 / 18.0
self.solution["C"].count = 1
self.solution["C"].freq = 1 / 18.0
self.solution["G"].count = 1
self.solution["G"].freq = 1 / 18.0
self.solution["-"].count = 1
self.solution["-"].freq = 1 / 18.0
self.pileup = "AAAAATTAATTAAA-AGC"
self.l = locus(pos=0)
for b in self.pileup:
self.l.update(b)