input_editase.py

#! /usr/bin/env python


#define acceptable input
rna = ['a','u','g','c','A','U','G','C',]
boxb = 'CCGGGAAAAAGUCCCGG'

#convert t to u
def makerna(seq):
	for x in range(len(seq)):
		if seq[x] == 't':
			seq[x] ='u'
		elif seq[x] == 'T':
			seq[x] = 'U'
		return seq

#check that all characters are acceptable rna code
def checkrna(seq):
	for char in list(seq):
	if char in rna:
		pass
	else:
		print "Something went wrong: Unexpected input(ACGU only please)!"
		sys.exit(0)

#take input of target
target = raw_input("Enter the target sequence (5'-3' up to 80bp): ")
target = makerna(target)
checkrna(target)

#take input of guide
guide = raw_input("Enter the Editase guide sequence (5'-3'): ")
guide = makerna(guide)
checkrna(guide)

#pt guide into correct orientation
revguide = guide[::-1]

#find boxB motif
boxbpos = revguide.find(boxb)
if boxbpos == -1:
	print "Something went wrong: No boxB motif was found in your guide!"
	sys.exit(0)
print "boxb offset:", boxbpos

row = guide[:boxbpos] + "   " + guide[boxbpos + 17:]

for x in range(len(revguide)):
	if revguide[x] == 'a' or 'A':
		compareguide[x] = 'U'
	elif revguide[x] == 'u' or 'U':
		compareguide[x] = 'A'
	elif revguide[x] == 'c' or 'C':
		compareguide[x] = 'G'
	elif revguide[x] == 'g' or 'G':
		compareguide[x] = 'C'
		
		
#distance into target that guide starts
best = 0
count = 0
for allign in range(len(target)-len(compareguide)):
	for x in range(len(compareguide)):
		if target[x] == compareguide[x]:
			count += 1
	if count > best:
		best = count
		offset = allign


print target
print str(offset * ' '),revguide

sctg_verify.py

#!/usr/bin/env python3
import os
file = open('unreplaced.txt', 'r')
i=0
for bits in file:
	file.seek(i)
	current = file.read(1)
	if current == 'A' or current =='T' or current == 'C' or current == 'G':
		i += 1
	else:
		print (current)
		print (i)
		i += 1