from Bio.Alphabet import IUPAC

from Bio.Data import IUPACData

from Bio.Seq import Seq

class TALrepeat:

A = 'LTPDQVVAIAS'

B = 'GGKQALETVQRLLPVLCQDHG'

C = 'GGKQALE'

def __init__(self, nucleotide, last=False):

self.last = last

if nucleotide.upper() == 'G' or nucleotide.upper() == 'R':

self.rvd = 'NN'

elif nucleotide.upper() == 'A':

self.rvd = 'NI'

elif nucleotide.upper() == 'T':

self.rvd = 'NG'

elif nucleotide.upper() == 'C':

self.rvd = 'HD'

elif nucleotide in IUPACData.ambiguous_dna_letters:

self.rvd = 'NS'

else:

self.rvd = None

def __str__(self):

return self.sequence()

def sequence(self):

if self.rvd is None:

return None

else:

if self.last:

return Seq(self.A + self.rvd + self.C, alphabet=IUPAC.protein)

else:

return Seq(self.A + self.rvd + self.B, alphabet=IUPAC.protein)

def template(self):

return Seq(self.A + 'XX' + self.B, alphabet=IUPAC.protein)

class TALE:

def __init__(self, target, upstream=None, downstream=None):

self.target = target

self.repeats = []

self.upstream = upstream

self.downstream = downstream

index = 0

for n in target:

index += 1

if index == len(target):

self.repeats.append(TALrepeat(n, True))

else:

self.repeats.append(TALrepeat(n))

def __str__(self):

return self.protein()

def protein(self):

sequence = self.upstream

for r in self.repeats:

sequence += r.sequence()

sequence += self.downstream

return sequence

def sequence(self):

return self.protein()

def repeat(self):

return self.repeats[0].template()

def n_repeats(self):

return len(self.repeats)