def testStopDouble(self):
'''test two stop codons.'''
ref = list(self.seq)
ref[-3] = "T"
for x in range(len(ref) - 3):
s = list(ref)
s[x] = "T"
r = snp2counts.countEffectsOnTranscript(s, ref)
self.assertEqual(r.ninserted_bases, 0)
self.assertEqual(r.ninserted_codons, 0)
self.assertEqual(r.ndeleted_bases, 0)
self.assertEqual(r.ndeleted_codons, 0)
self.assertEqual(r.noframe_codons, 0)
self.assertEqual(r.nwrong_frames, 0)
self.assertEqual(r.ncorrected_frames, 0)
if x % 3 == 0:
self.assertEqual(r.nstops, 2)
self.assertEqual(r.first_stop, x // 3)
# ignore last incomplete codon
self.assertEqual(r.nstop_codons, 1)
else:
self.assertEqual(r.nstops, 1)
self.assertEqual(r.first_stop, self.ncodons - 1)
self.assertEqual(r.nstop_codons, 0)
def testStop(self):
'''test one stop codon.'''
for x in range(len(self.seq)):
s = list(self.seq)
s[x] = "T"
r = snp2counts.countEffectsOnTranscript(s, self.seq)
# print s, str(r)
self.assertEqual(r.ninserted_bases, 0)
self.assertEqual(r.ninserted_codons, 0)
self.assertEqual(r.ndeleted_bases, 0)
self.assertEqual(r.ndeleted_codons, 0)
self.assertEqual(r.noframe_codons, 0)
self.assertEqual(r.nwrong_frames, 0)
self.assertEqual(r.ncorrected_frames, 0)
self.assertEqual(r.nsynonymous_codons, 0)
if x % 3 == 0:
self.assertEqual(r.nstops, 1)
self.assertEqual(r.first_stop, x // 3)
# ignore last incomplete codon
if x < self.length - 3:
self.assertEqual(r.nstop_codons, 1)
self.assertEqual(r.nnonsynonymous_codons, 0)
else:
self.assertEqual(r.nstops, 0)
self.assertEqual(r.first_stop, self.ncodons)
self.assertEqual(r.nstop_codons, 0)
self.assertEqual(r.nnonsynonymous_codons, 1)
def testMutation(self):
'''test synonymous/nonsynonymous mutation.'''
for x in range(len(self.seq)):
s = list(self.seq)
# aaa = K, aag = N
s[x] = "G"
r = snp2counts.countEffectsOnTranscript(s, self.seq)
self.assertEqual(r.ninserted_bases, 0)
self.assertEqual(r.ninserted_codons, 0)
self.assertEqual(r.ndeleted_bases, 0)
self.assertEqual(r.ndeleted_codons, 0)
self.assertEqual(r.noframe_codons, 0)
self.assertEqual(r.nwrong_frames, 0)
self.assertEqual(r.ncorrected_frames, 0)
self.assertEqual(r.nstops, 0)
self.assertEqual(r.first_stop, self.ncodons)
self.assertEqual(r.nstop_codons, 0)
if x % 3 == 2:
self.assertEqual(r.nsynonymous_codons, 1)
self.assertEqual(r.nnonsynonymous_codons, 0)
else:
self.assertEqual(r.nsynonymous_codons, 0)
self.assertEqual(r.nnonsynonymous_codons, 1)
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
r = snp2counts.countEffectsOnTranscript(s, self.seq)
# print s, str(r)
self.assert_(r.ndeleted_codons + r.nunaffected_codons + r.nincomplete_codons +
r.nnonsynonymous_codons + r.nsynonymous_codons + r.nstop_codons <=
self.ncodons)
self.assertEqual(r.ninserted_bases, 0)
self.assertEqual(r.ninserted_codons, 0)
self.assertEqual(r.ndeleted_bases, todelete)
codon_start = (x // 3) * 3
codon_end = x + l + (3 - (x + l) % 3) % 3
affected_codons = (codon_end - codon_start) // 3
deletion_codon_start = x + (3 - (x % 3)) % 3
deletion_codon_end = min(self.length, ((x + l) // 3) * 3)
# subtract fully deleted codons
deleted_codons = max(
0, (deletion_codon_end - deletion_codon_start) // 3)
self.assertEqual(r.ndeleted_codons, deleted_codons)
inframe = x // 3
# delete in-frame, multiple of 3
if x % 3 == 0 and todelete % 3 == 0:
self.assertEqual(r.noframe_codons, 0)
self.assertEqual(r.nwrong_frames, 0)
self.assertEqual(r.ncorrected_frames, 0)
self.assertEqual(r.nsynonymous_codons, 0)
# delete out-of-frame, multiple of 3
elif x % 3 != 0 and todelete % 3 == 0:
self.assertEqual(
r.noframe_codons, affected_codons - deleted_codons)
self.assertEqual(r.nwrong_frames, 1)
self.assertEqual(r.ncorrected_frames, 1)
# delete, but not multiple of 3
else:
self.assertEqual(
r.noframe_codons, self.ncodons - inframe - deleted_codons)
self.assertEqual(r.nwrong_frames, 1)
self.assertEqual(r.ncorrected_frames, 0)
# self.assertEqual( r.nsynonymous_codons,
# self.ncodons - r.nincomplete_codons - inframe - deleted_codons)
self.assertEqual(r.first_stop, (self.length - todelete) // 3)
# self.assertEqual( r.nunaffected_codons, self.ncodons - (int(math.ceil( (x + todelete) / 3.0)) - x // 3) )
self.assertEqual(r.nnonsynonymous_codons, 0)
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]
r = snp2counts.countEffectsOnTranscript(s, self.seq)
# print s, str(r)
self.assertEqual(r.ninserted_bases, l)
if l % 3 == 0:
self.assertEqual(r.ninserted_codons, l // 3)
self.assertEqual(r.nwrong_frames, 0)
self.assertEqual(r.ndeleted_bases, 0)
self.assertEqual(r.ndeleted_codons, 0)
unaffected = x // 3
if l % 3 == 0:
self.assertEqual(r.noframe_codons, 0)
self.assertEqual(r.ncorrected_frames, 0)
self.assertEqual(r.nunaffected_codons, 20)
self.assertEqual(r.nsynonymous_codons, 0)
else:
self.assertEqual(r.noframe_codons, self.ncodons - x / 3)
self.assertEqual(r.ncorrected_frames, 0)
self.assertEqual(r.nunaffected_codons, unaffected)
self.assertEqual(r.first_stop, (self.length + l) // 3)
self.assertEqual(r.nnonsynonymous_codons, 0)
def testFrameCorrectionAdacent(self):
'''test frame correction within a codon for
two adjacent bases.
Strictly speaking this should not happen as these
would be called as substitutions.
'''
return
for l in range(1, 7):
for x in range(len(self.seq) - l):
s = list(self.seq)
todelete = l
toinsert = l
for y in range(x, x + todelete):
s[y] = ""
s[x + todelete] = "A" * toinsert + s[x + todelete]
ncodons = self.ncodons
# print l,x,todelete, toinsert
# print s
r = snp2counts.countEffectsOnTranscript(s, self.seq)
# print str(r)
self.assert_(r.ndeleted_codons + r.nunaffected_codons + r.nincomplete_codons +
r.nnonsynonymous_codons + r.nsynonymous_codons + r.nstop_codons <=
self.ncodons)
self.assertEqual(r.ninserted_codons, 0)
if (x + todelete) % 3 != 0:
self.assertEqual(r.ninserted_bases, 0)
self.assertEqual(r.ndeleted_bases, 0)
self.assertEqual(r.noframe_codons, 0)
else:
self.assertEqual(r.ninserted_bases, toinsert)
self.assertEqual(r.ndeleted_bases, todelete)
self.assertEqual(r.noframe_codons, 2)
if x % 3 == 0 and todelete % 3 == 0:
self.assertEqual(r.ndeleted_codons, todelete / 3)
else:
self.assertEqual(r.ndeleted_codons, 0)
self.assert_(r.noframe_codons <= self.ncodons)
self.assertEqual(r.nwrong_frames, 1)
self.assertEqual(r.ncorrected_frames, 1)
self.assertEqual(r.ntruncated_codons_stop, 0)
# self.assertEqual( r.nunaffected_codons, self.ncodons )
self.assertEqual(r.nsynonymous_codons, 0)
self.assertEqual(r.nnonsynonymous_codons, 0)
def testEmpty(self):
r = snp2counts.countEffectsOnTranscript(self.seq, self.seq)
self.assertEqual(r.ninserted_bases, 0)
self.assertEqual(r.ninserted_codons, 0)
self.assertEqual(r.ndeleted_bases, 0)
self.assertEqual(r.ndeleted_codons, 0)
self.assertEqual(r.noframe_codons, 0)
self.assertEqual(r.nwrong_frames, 0)
self.assertEqual(r.ncorrected_frames, 0)
self.assertEqual(r.first_stop, self.ncodons)
self.assertEqual(r.nstop_codons, 0)
self.assertEqual(r.nstops, 0)
self.assertEqual(r.nunaffected_codons, self.ncodons)
self.assertEqual(r.nsynonymous_codons, 0)
self.assertEqual(r.nnonsynonymous_codons, 0)
def testFrameCorrection(self):
'''test frame correction within a codon for
two adjacent bases.
Strictly speaking this should not happen as these
would be called as substitutions.
'''
return
for l in range(1, 7):
for offset in range(1, 5):
for x in range(len(self.seq) - (l + offset)):
s = list(self.seq)
todelete = l
toinsert = l
for y in range(x, x + todelete):
s[y] = ""
codon_start = (x // 3) * 3
codon_end = ((x + offset + todelete) // 3 + 1) * 3
s[x + todelete + offset] = "A" * toinsert + s[x + todelete]
ncodons = self.ncodons
# print "l=",l,"x=",x,"offest=",offset,"del=",todelete,
# "ins=",toinsert, "start=",codon_start, "end=", codon_end
naffected_codons = (codon_end - codon_start) // 3
if todelete % 3 == 0 and (x + todelete) // 3 != (x + todelete + offset) // 3:
# affected codons reduced, if offset includes full
# codons
naffected_codons -= (x + todelete +
offset) // 3 - (x + todelete) // 3
# if offset > 3:
# naffected_codons -= 1
# print s
r = snp2counts.countEffectsOnTranscript(s, self.seq)
# print str(r)
self.assertEqual(r.ninserted_codons, l // 3)
self.assertEqual(r.ninserted_bases, toinsert)
self.assertEqual(r.ndeleted_bases, todelete)
if l + offset <= 2 and x % 3 == 0 or (x % 3 == 0 and l % 3 == 0):
# within codon correction
self.assertEqual(r.noframe_codons, 0)
self.assertEqual(r.nwrong_frames, 0)
self.assertEqual(r.ncorrected_frames, 0)
else:
# between codon correction
self.assertEqual(r.ninserted_bases, toinsert)
self.assertEqual(r.ndeleted_bases, todelete)
self.assertEqual(r.noframe_codons, naffected_codons)
self.assertEqual(r.nwrong_frames, 1)
self.assertEqual(r.ncorrected_frames, 1)
if x % 3 == 0 and todelete % 3 == 0:
self.assertEqual(r.ndeleted_codons, todelete / 3)
else:
self.assertEqual(r.ndeleted_codons, 0)
self.assert_(r.noframe_codons <= self.ncodons)
self.assertEqual(r.first_stop, 0)
# self.assertEqual( r.nunaffected_codons, self.ncodons )
self.assertEqual(r.nsynonymous_codons, 0)
self.assertEqual(r.nnonsynonymous_codons, 0)