def mismatch_center(off, effect='x'):
i = len(off) // 2
context = off[i - 1:i + 2]
if len(off) < 3:
raise RnaDesignError
if au_au_pattern.match(context):
mut_table = au_au_mismatches
elif au_gc_pattern.match(context):
mut_table = au_gc_mismatches
elif gc_gc_pattern.match(context):
mut_table = gc_gc_mismatches
else:
raise AssertionError
if effect == 'x':
effector = rc(mutate(off, i, c(mut_table[off[i]])))
on = rc(effector)
elif effect == 'o':
on = mutate(off, i, mut_table[c(off[i])])
effector = rc(off)
return Mutant(effector, on, off)
def wobble_all(off, effect='x'):
# Find all the positions where a wobble base pair could be made, i.e. all
# the positions in the "off" sequence that are either G or U.
if effect == 'x':
effector = c(off)
for i, bp in enumerate(off):
if bp == 'G':
effector = mutate(effector, i, 'U')
if bp == 'U':
effector = mutate(effector, i, 'G')
on = rc(effector)
elif effect == 'o':
on = off
for i, bp in enumerate(off):
if bp == 'A':
on = mutate(on, i, 'G')
if bp == 'C':
on = mutate(on, i, 'U')
effector = rc(off)
else:
raise ValueError("Unknown effect: '{}'".format(effect))
return Mutant(effector, on, off)
def bulge(off, effect='x', nuc='A'):
if effect == 'x':
effector = insert(rc(off), len(off) // 2, nuc)
on = rc(effector)
if effect == 'o':
on = insert(off, len(off) // 2, nuc)
effector = rc(off)
return Mutant(effector, on, off)
def wobble(off, effect='x', location='center'):
# Find all the positions where a wobble base pair could be made, i.e. all
# the positions in the "off" sequence that are either G or U.
if effect == 'x':
gu_iter = re.finditer('[GU]', off)
elif effect == 'o':
gu_iter = re.finditer('[AC]', off)
else:
raise ValueError("Unknown effect: '{}'".format(effect))
gus = [x.start() for x in gu_iter]
if not gus:
raise RnaDesignError("No G or U nucleotides in input sequence.")
# Decide where to insert the wobble base pair based on the location
# argument. The default is to mutate the center-most position, but the
# user can choose to mutate the inner- or outer-most positions as well.
if location == 'center':
N = D = len(off)
for i in gus:
d = abs(i - N / 2)
if d < D: gu, D = i, d
elif location == 'edge':
# We'll assume that the edge is on the left, here.
gu = gus[0]
elif location == 'non-edge':
gu = gus[-1]
else:
raise ValueError("Unknown location: '{}'".format(location))
# Create "on" and "effector" sequences that will have the desired effect.
# The effect "x" means more cutting is desired, so the interaction between
# the "effector" and "off" sequences has to be weakened. The effect "o"
# means that less cutting is desired, so the interaction between the
# "effector" and "on" sequences has to be weakened.
if effect == 'x':
effector = r(mutate(c(off), gu, {'G': 'U', 'U': 'G'}[off[gu]]))
on = rc(effector)
elif effect == 'o':
on = mutate(off, gu, {'C': 'U', 'A': 'G'}[off[gu]])
effector = rc(off)
return Mutant(effector, on, off)
def mismatch(off, pattern, mutations, effect='x', location='center'):
import re
matches = pattern.finditer(off)
indices = [x.start() + 1 for x in matches]
if not indices: raise RnaDesignError
i = pick_location(location, indices, len(off))
if effect == 'x':
effector = rc(mutate(off, i, c(mutations[off[i]])))
on = rc(effector)
elif effect == 'o':
on = mutate(off, i, mutations[c(off[i])])
effector = rc(off)
return Mutant(effector, on, off)