I am TRYING to write a program that finds restriction sites in a DNA file and returns a picture and information box of the enzyme which cuts it. My problems are;
a) I have no idea if my program works past opening the file directory.
b) I dont know how to iterate through the file 6 characters at a time, moving 1 character along each time. I need to do this, then use the dictionary to get the enzyme that corresponds to the found restriction site....
I have included my code so far. If someone can atleast tell me how to check if my code is working that would be PERFECT.
from Tkinter import *
from tkMessageBox import *
from tkFileDialog import *
#An example library of restriction enzymes and their recognition sites
site_enz= {'GAATTC':'EcoRI','GGATTC':'BamHI','AAGCTT':'HindIII',
'CCCGGG':'Smal','GATATC':'EcoRV'}
class RestrictionSites (object):
"""A class to find splice sites within an RNA sequence chosen by the user"""
def __init__(self, master):
self.master = master
self.frame = Frame(master)
self.frame.pack()
# selecting the image to use
self.image = PhotoImage(file="Opening Picture.gif")
# create a canvas that fits the image used
self.canvas = Canvas(self.frame,
width=self.image.width(),
height=self.image.height())
# aligning the image to the top left corner of the canvas
self.canvas.create_image(0,0, anchor=NW, image=self.image)
self.canvas.pack()
# now I want to add a button underneath, cannot but canvas and
# button on the same frame so need to create a new frame for button
self.button_panel = Frame(self.frame)
self.button_panel.pack(side=TOP)
# sets the width and position of the start button
self.start_button = Button(self.button_panel,
text="Click to upload a single stranded DNA sequence 5'-3'", width=100, command=self.startbutton)
self.start_button.pack()
def startbutton (self):
self.FindFile()
def FindFile (self):
#Save as dialog
filename = askopenfilename(parent=root,initialdir="/",title='Please select a directory')
#When I need the file I refer to this bit
my_file=open(filename,'r')
temp = my_file.read().upper()
my_file.close()
def valid_input(self):
#Checks file is a valid DNA sequence
while True:
self.file=self.FindFile()
self.file=self.file.upper()
#Only these bases allowed
good_bases = "ATCG"
temp_sequence = ''
for base in self.file:
if base in good_bases:
temp_sequence += base
self.file = temp_sequence
#Flag for error- assume OK at the start.
bad_input = False
#Check each base.
for base in self.file:
if base in good_bases:
#Ok so far, check next base.
continue
else:
#Not an RNA base, so flag the error.
bad_input= True
#Give the user the bad news
print 'Sorry - that is not a DNA sequence, please try again.'
#break from the 'for' loop
break
#By this stage the sequence has been checked.
#If all is awell, break form the 'while' loop.
if bad_input ==False:
break
#Otherwise the 'while' loop will go back for re-input.
return self.file
def find_site (self):
"""This function checks if there is a restriction site in the DNA"""
if site_enz.has_key(site)==False:
return '?'
return site_enz.get(site)
def find_rest_site( sequence, init_pos, restriction_site):
#function to find six-base restriction sites in a DNA sequence
#self.findfile is a string containing the DNA sequence
#init_pos is the position to start searching from (to start from the beginning, set it to 0)
#restriction_site is a string containing the sequence sought....
#but i need to get the site from the dictionary
#the function returns a list of positions where the restriction site was found
#if none are found then the list will be empty
list_of_sites=[]
end = len(sequence)-6
for pointer in range(init_pos, end):
sixer = self.FindFile[pointer:pointer+6]
if sixer==self.find_site:
list_of_sites.append(pointer)
print list_of_sites
return list_of_sites
#Main program
#this root widget sets the title of the screen
root = Tk()
root.title
#set this class to be an object
app= RestrictionSites(root)
#loops the class until the event happens and makes everything visible.
root.mainloop()
