def testDeletion( self ):
'''test single deletion.'''
for l in range(1,7):
for x in range(0,len(self.seq)):
s = list(self.seq)
todelete = min(l, self.length - x )
for y in range(x,x+todelete): s[y] = ""
ncodons = self.ncodons - todelete // 3
i = list(snp2counts.iterateOverFrames( s ))
codon_start = (x // 3) * 3
codon_end = min(self.length, x + l + (3 - (x + l) % 3) % 3)
result = []
if codon_start > 0: result.append( [True, 0, codon_start] )
if todelete % 3 == 0:
if x % 3 != 0:
result.append( [False, codon_start, codon_end] )
if codon_end < self.length: result.append( [True, codon_end, self.length] )
else:
result.append( [True, codon_start, self.length] )
else:
o = codon_start
if todelete > 3 and x % 3 == 0:
o = codon_start + (todelete // 3) * 3
result.append( [True, codon_start, o] )
result.append( [False, o, codon_end ] )
result.append( [False, codon_end, self.length ] )
result = self.merge( result )
self.assertEqual( i, result )
def testInsertion( self ):
'''test single insertion.'''
for l in range(1,7):
for x in range(len(self.seq)):
s = list(self.seq)
s[x] = "A"*l + s[x]
i = list(snp2counts.iterateOverFrames( s ))
result = []
codon_start = (x // 3) * 3
if codon_start > 0: result.append( [True, 0, codon_start] )
if l % 3 == 0:
result.append( [True, 0, self.length ] )
else:
result.append( [False, codon_start, self.length ] )
result = self.merge( result )
self.assertEqual( i, result )
def testDeletion(self):
'''test single deletion.'''
for l in range(1, 7):
for x in range(0, len(self.seq)):
s = list(self.seq)
todelete = min(l, self.length - x)
for y in range(x, x + todelete):
s[y] = ""
ncodons = self.ncodons - todelete // 3
i = list(snp2counts.iterateOverFrames(s))
codon_start = (x // 3) * 3
codon_end = min(self.length, x + l + (3 - (x + l) % 3) % 3)
result = []
if codon_start > 0:
result.append([True, 0, codon_start])
if todelete % 3 == 0:
if x % 3 != 0:
result.append([False, codon_start, codon_end])
if codon_end < self.length:
result.append([True, codon_end, self.length])
else:
result.append([True, codon_start, self.length])
else:
o = codon_start
if todelete > 3 and x % 3 == 0:
o = codon_start + (todelete // 3) * 3
result.append([True, codon_start, o])
result.append([False, o, codon_end])
result.append([False, codon_end, self.length])
result = self.merge(result)
self.assertEqual(i, result)
def testInsertion(self):
'''test single insertion.'''
for l in range(1, 7):
for x in range(len(self.seq)):
s = list(self.seq)
s[x] = "A" * l + s[x]
i = list(snp2counts.iterateOverFrames(s))
result = []
codon_start = (x // 3) * 3
if codon_start > 0:
result.append([True, 0, codon_start])
if l % 3 == 0:
result.append([True, 0, self.length])
else:
result.append([False, codon_start, self.length])
result = self.merge(result)
self.assertEqual(i, result)
