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biotype.py
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import time
from tkinter import *
import tkinter.filedialog
import random
import glob
root = Tk()
# Colors
darkish = '#%02x%02x%02x' % (29, 30, 38)
whitish = '#%02x%02x%02x' % (214, 216, 218)
code_green = '#%02x%02x%02x' % (80, 230, 70)
greyOut = '#%02x%02x%02x' % (110, 110, 110)
pink = '#%02x%02x%02x' % (254, 102, 238)
cyan = '#%02x%02x%02x' % (50, 250, 250)
blueish = '#%02x%02x%02x' % (143, 220, 210)
whiteblue = '#%02x%02x%02x' % (173, 250, 220)
orangetxt = '#%02x%02x%02x' % (250, 140, 0)
red = '#%02x%02x%02x' % (239, 30, 0)
lightgreen = '#%02x%02x%02x' % (135, 255, 117)
greygreen = '#%02x%02x%02x' % (160, 190, 140)
black = '#%02x%02x%02x' % (20, 20, 20)
red = '#%02x%02x%02x' % (255, 60, 60)
green = '#%02x%02x%02x' % (60, 255, 60)
blue = '#%02x%02x%02x' % (60, 60, 255)
orange = '#%02x%02x%02x' % (250, 140, 0)
yellow = '#%02x%02x%02x' % (200, 240, 70)
colors = ["red", "green", "blue", "orange", "yellow", cyan, pink, lightgreen, blueish]
root.configure(bg=darkish)
root.configure(cursor="arrow")
Label(root, text="BioType", font='Futura 30 bold', bg=darkish, fg=whitish).grid(row=0, column=1)
Label(root, text="Construction File Visualizer", font='Futura 15', bg=darkish, fg=whitish).grid(row=1, column=1)
sidebar = Frame(root, bg=darkish, width=60, height=30)
sidebar.grid(row=3, column=0)
sidebar = Frame(root, bg=darkish, width=60, height=30)
sidebar.grid(row=3, column=2)
editor = Text(root, font='Menlo 18', bg=darkish, fg=whitish, width=100, height=30,
highlightbackground=greyOut, highlightthickness=2, insertbackground=whitish, insertwidth=4,
cursor="arrow")
editor.grid(row=6, column=1)
# Inserts the basic construction template
fileStr = open('Basic_Part_Construction.txt').read()
editor.insert(INSERT, fileStr)
tags = ["grey", "pink", "green", "cyan", "whiteblue", "orange",
"red", "lightgreen", "greygreen", "hRed", "default", "error"]
enzymes = [] # The list of all enzymes supported
def reverse(s):
strng = ""
for i in s:
strng = i + strng
return strng
class Sequence: # The Sequence class (every DNA sequence, with its name, end position
name = ""
namePos = ""
sequence = ""
endPos = ""
sequences = [] #All the sequences known
# Change the name of the sequence
def changeName(self, newName):
print(self.name + " => " + newName)
editor.delete(self.namePos, self.namePos.__add__("+ " + str(len(self.name)) + " chars"))
editor.insert(self.namePos, newName)
self.name = newName
# Update the sequence to a new sequence
def updateSeq(self, newSeq):
editor.delete(self.namePos.__add__(" lineend + 1 chars"),
self.endPos)
editor.insert(self.namePos.__add__(" lineend + 1 chars"), newSeq)
self.sequence = newSeq
# Method to get the specific Sequence instance from the name
def get(self, name):
Sequence.initSequences(self)
for s in Sequence.sequences:
if s.name in name or name in s.name:
return s
return None
# For PCR
def addPrimerF(self, primer):
print()
def addPrimerR(self, primer):
print()
# Greys out the sequence after the instruction has been completed, for instance
def greyOut(self):
editor.delete(self.namePos.__add__("- 1 chars"))
editor.insert(self.namePos.__add__("- 1 chars"), "#")
editor.insert(self.namePos.__add__("- 1 chars + 1 lines"), "#")
editor.tag_add("grey", self.namePos.__add__("- 1 chars"), self.endPos)
# No functionality ATM
def showReverseCompliment(self):
print()
# Initializes all the sequences from the text and appends them to Sequence.sequences[]
def initSequences(self):
Sequence.sequences = []
pos = editor.search(">", '1.0', stopindex=END, regexp=True)
while pos != '':
s = Sequence()
s.namePos = pos.__add__("+ 1 chars")
if pos != '':
pos = pos.__add__("+ 1 chars")
while (not util.isCrap(pos, editor)) and (editor.get(pos) != "."):
s.name += editor.get(pos)
pos = pos.__add__(" + 1 chars")
finalPos = editor.search(".", pos, stopindex=END)
if finalPos != '':
s.endPos = finalPos
s.sequence = editor.get(s.namePos.__add__(" lineend + 1 chars"), finalPos.__add__(" -1 chars"))
else:
s.endPos = END
s.sequence = editor.get(s.namePos.__add__(" lineend + 1 chars"), END)
Sequence.sequences.append(s)
pos = editor.search(">", pos.__add__(" + 1 chars"), stopindex=END, regexp=True)
# The Gene class specifies what part of the sequence gets highlighted - used as a visual aid for developing parts
class Gene:
genes = []
name = ""
color = ""
pos = ""
fromPos = 0
toPos = 0
sequence = Sequence()
size = 0
def initGenes(self):
pos = editor.search("@", '1.0', END)
Sequence.initSequences(Sequence)
while (pos != ''):
gene = Gene()
pos = pos.__add__("+ 1 chars")
gene.pos = pos
gene.name = util.getVarName(Util, pos)
pos = pos.__add__("+ " + str(gene.name.__len__()) + " chars")
while Util.isCrap(pos, editor) & (pos.__add__("+ 1 chars") != ''):
pos = pos.__add__("+ 1 chars")
gene.fromPos = util.getVarName(Util, pos)
pos = pos.__add__("+ " + str(gene.fromPos.__len__()) + " chars")
while Util.isCrap(pos, editor) & (pos.__add__("+ 1 chars") != ''):
pos = pos.__add__("+ 1 chars")
gene.toPos = util.getVarName(Util, pos)
gene.size = int(gene.toPos)-int(gene.fromPos)
pos = pos.__add__("+ " + str(gene.toPos.__len__()) + " chars")
while Util.isCrap(pos, editor) & (pos.__add__("+ 1 chars") != ''):
pos = pos.__add__("+ 1 chars")
gene.color = util.getVarName(Util, pos)
pos = pos.__add__("+ " + str(gene.color.__len__()) + " chars")
while Util.isCrap(pos, editor) & (pos.__add__("+ 1 chars") != ''):
pos = pos.__add__("+ 1 chars")
gene.sequence = Sequence.get(Sequence, util.getVarName(Util, pos))
if (gene.sequence != 'null') :
Gene.genes.append(gene)
pos = editor.search("@", pos.__add__(" lineend + 1 chars"), END)
# Greys out the gene
def greyOut(self):
editor.insert(self.pos, '#')
# Prints all the genes to the console
def printToString(self):
print(str(Gene.genes.__len__())+ " :")
for g in Gene.genes :
print(g.name + ", " + g.sequence.name + ", " + g.color + "(" + g.fromPos + "..." + g.toPos + ")")
# Util handles useful methods for other functions
class Util:
contents = ""
cur_name = ""
# Updates bp place in sequence
def updateBpToSelection(self, label):
label.config(text="§ ")
for s in Sequence.sequences:
numUseless = 0
for letter in editor.get(index1=s.namePos.__add__(" lineend + 1 chars"),
index2=INSERT):
if letter == "|":
numUseless += 1
if (editor.compare(INSERT, '<=', s.endPos)) & (editor.compare(s.namePos.__add__(" lineend + 1 chars"),
'<=', INSERT)):
label.config(text="§ " + str(len(editor.get(index1=s.namePos.__add__(" lineend + 1 chars"),
index2=INSERT))-numUseless) + "bp")
# updates the text in the corner to a description of whatever is currently being clicked on, with the color
def updateColorToSelection(self, label, l2, l3):
tag = editor.tag_names(INSERT) # gets the tags at the current click pos
if tag.__len__() > 0: # TODO: Show multiple genes and/or enzymes located at the same spot at the same time
if "pink" in tag :
label.config(text="• Sequence", fg=pink)
l2.config(text=" Sequence can be a/c/t/g")
l3.config(text="")
if "_" in tag[0]:
name = "• " + tag[0][1:]
c = editor.tag_cget(tag[0], "background")
if c == '':
c = whitish
label.config(text=name, fg=c)
if (Enzyme.get(Enzyme, tag[0][1:]) != "null") :
l2.config(text=" "+Enzyme.get(Enzyme, tag[0][1:]).type+", site : "+Enzyme.get(Enzyme, tag[0][1:])
.siteCut)
space = ""
space += " " * len("tttttttttttttt" + Enzyme.get(Enzyme, tag[0][1:]).type + " ")
l3.config(text=space+Enzyme.get(Enzyme, tag[0][1:])
.siteCut2)
if "lightgreen" in tag :
label.config(text="• Plasmid", fg=lightgreen)
l2.config(text=" Call something 'pName' to make it a plasmid")
l3.config(text="")
if "orangetxt" in tag :
label.config(text="• Click anything for more info", fg=whitish)
l2.config(text="")
l3.config(text="")
if "cyan" in tag:
label.config(text="• Instruction", fg=whiteblue)
l2.config(text=" Supports PCR/Ligate/Digest/Transform/PCA")
l3.config(text="")
if "blueish" in tag:
label.config(text="• Feature", fg=whiteblue)
l2.config(text=" Declare a feature with '@[name] [fromBP] [toBP] [color] [sequence]'")
l3.config(text="")
else:
for g in Gene.genes:
if g.name in tag:
name = "• Feature: " + g.name
c = editor.tag_cget(tag[0], "foreground")
label.config(text=name, fg=c)
l2.config(text=" size: " + str(int(g.toPos) - int(g.fromPos)) + "bp")
l3.config(text="")
for e in enzymes:
if e.name in tag:
name = "• " + e.name
c = e.color
label.config(text=name, fg=c)
l2.config(text=" " + e.type + ", site : " + e.siteCut)
space = ""
space += " " * len("tttttttttttttt" + e.type + " ")
l3.config(text=space + e.siteCut2)
else :
label.config(text="• Click anything for more info", fg=whitish)
l2.config(text="")
l3.config(text="")
def rev_complement(self, str): # Gets the reverse compliment of any sequence, ie atcg => tagc
revStr = ""
for i in str :
if (i=='a') :
revStr += 't'
if (i=='t') :
revStr += 'a'
if (i=='c') :
revStr += 'g'
if (i=='g') :
revStr += 'c'
if (i=='A') :
revStr += 'T'
if (i=='T') :
revStr += 'A'
if (i=='C') :
revStr += 'G'
if (i=='G') :
revStr += 'C'
if (i=='n') :
revStr = "n" + revStr
return reverse(revStr)
# superscript for reference ᵃ ᶜ ᵗ ᵍ
def superscript(self, str): # Converts the letters a t c g to superscript equivalents, for rendering sticky ends
newStr = ""
for i in str :
if (i=='a') :
newStr += 'ᵃ'
if (i=='c') :
newStr += 'ᶜ'
if (i=='t') :
newStr += 'ᵗ'
if (i=='g') :
newStr += 'ᵍ'
if (i=='A') :
newStr += 'ᵃ'
if (i=='C') :
newStr += 'ᶜ'
if (i=='T') :
newStr += 'ᵗ'
if (i=='G') :
newStr += 'ᵍ'
return newStr
def desuperscript(self, str): # Converts the letters a t c g to superscript equivalents, for rendering sticky ends
newStr = ""
for i in str :
if (i=='ᵃ') :
newStr += 'a'
if (i=='ᶜ') :
newStr += 'c'
if (i=='ᵗ') :
newStr += 't'
if (i=='ᵍ') :
newStr += 'g'
return newStr
def getVarName(self, pos): # getVarName will take in a position in the text and find the next variable name
var = ""
while not Util.isCrap(pos, editor):
var += editor.get(pos)
pos = pos.__add__("+ 1 chars")
return var
def getVarNameStr(self, pos, str, WITHSPACE): # Same as above but for a string instead of a Text object
var = ""
if WITHSPACE :
if str.__len__() > pos :
while (not Util.isCrapStr(self, pos, str) )| (str[pos] == " "):
if str[pos] == " " :
var += "-"
else :
var += str[pos]
pos += 1
else :
while (not Util.isCrapStr(self, pos, str)):
var += str[pos]
pos += 1
return var
def isPlasmid(pos, txt): # if a sequence starts with a lowercase p and then a capital, it's init. as a plasmid
if (txt.get(pos) == "p") & (txt.get(pos.__add__("+ 1 chars")).isupper()):
return True
def seqColor(pos, txt): # if plasmid then the color is green, vs pink otherwise
if util.isPlasmid(pos, txt):
return "lightgreen"
else:
return "pink"
def isCrap(pos, txt): # if text is useless shit we don't care about
if (txt.get(pos) == " ") | (txt.get(pos) == "(") | (txt.get(pos) == ")") \
| (txt.get(pos) == ",") | (txt.get(pos) == "/") | (txt.get(pos) == ",") | (txt.get(pos) == "+") | (
txt.get(pos) == "\n"):
return True
else:
return False
def isCrapStr (self, pos, str): # same as above for a string instead of a Text obj
if (pos >= str.__len__()) :
return True
if (str[pos] == " ") | (str[pos] == "(") | (str[pos] == ")") \
| (str[pos] == ",") | (str[pos] == "/") | (str[pos] == ",") | (str[pos] == "+")| (str[pos] == ".") | (
str[pos] == "\n"):
return True
else:
return False
def geneStyle(self): # Renders the genes
for gene in Gene.genes:
editor.tag_config(gene.name, foreground=gene.color)
pos = editor.search(gene.sequence.sequence[int(gene.fromPos):int(gene.toPos)], '1.0', stopindex=END,
regexp=True)
while (pos != ''):
for g in Gene.genes :
if gene.size < g.size:
editor.tag_remove(g.name, pos, pos.__add__("+ " + str(int(gene.toPos)-int(gene.fromPos)) + " chars"))
editor.tag_add(gene.name, pos, pos.__add__("+ " + str(int(gene.toPos)-int(gene.fromPos)) + " chars"))
pos = pos.__add__("+ 1 chars")
seq = gene.sequence.sequence[int(gene.fromPos):]
seq = seq[:int(gene.toPos)]
pos = editor.search(seq, pos.__add__("+ 1 chars"),
stopindex=END)
def textStyle(self, txt): # Renders the 'IDE'
txt.tag_config("grey", foreground=greyOut)
txt.tag_config("pink", foreground=pink)
txt.tag_config("green", foreground=code_green, underline=True)
txt.tag_config("cyan", foreground=cyan)
txt.tag_config("whiteblue", foreground=whiteblue)
txt.tag_config("orangetxt", foreground=orangetxt)
txt.tag_config("red", foreground=red)
txt.tag_config("lightgreen", foreground=lightgreen)
txt.tag_config("greygreen", foreground=greygreen)
txt.tag_config("blueish", foreground=blueish)
txt.tag_config("hRed", background=red)
txt.tag_config("default", foreground=whitish, background=darkish)
txt.tag_config("error", foreground=red, underline=True)
txt.tag_config("sticky", font="Futura 12")
txt.tag_config("stickyOnCompliment", font="Futura 12", underline=True)
for t in tags:
txt.tag_remove(t, '1.0', END)
for e in enzymes:
txt.tag_remove(e.name, '1.0', END)
txt.tag_remove("_" + e.name, '1.0', END)
pos = txt.search(r"-|>|{|}|@|\|", '1.0', stopindex=END, regexp=True)
while pos != '':
txt.tag_add("grey", pos)
pos = txt.search(r"-|>|{|}|@|\|", pos.__add__("+ 1 chars"), stopindex=END, regexp=True)
pos = txt.search(r"Ligate|Digest|PCR|PCA|Transform", '1.0', stopindex=END, regexp=True)
while pos != '':
while (txt.get(pos) != "") & (txt.get(pos) != " ") & (txt.get(pos) != "\n"):
txt.tag_add("cyan", pos)
pos = pos.__add__("+ 1 chars")
color = util.seqColor(pos, txt)
while (txt.get(pos.__add__("+ 1 chars")) != txt.get(pos.__add__(" lineend"))):
while (util.isCrap(pos, txt)):
pos = pos.__add__("+ 1 chars")
color = util.seqColor(pos, txt)
if (txt.get(pos) == "a") & (txt.get(pos.__add__("+ 1 chars")) == "n") & \
(txt.get(pos.__add__("+ 2 chars")) == "d") & (txt.get(pos.__add__("+ 3 chars")) == " "):
pos = pos.__add__("+ 4 chars")
color = util.seqColor(pos, txt)
if (txt.get(pos) == "o") & (txt.get(pos.__add__("+ 1 chars")) == "n") & \
(txt.get(pos.__add__("+ 3 chars")) == " "):
pos = pos.__add__("+ 3 chars")
color = util.seqColor(pos, txt)
else:
txt.tag_add(color, pos)
pos = pos.__add__("+ 1 chars")
if not util.isCrap(pos, txt):
txt.tag_add(color, pos)
pos = txt.search(r"Ligate|Digest|PCR|PCA|Transform", pos.__add__("+ 1 chars"), stopindex=END, regexp=True)
pos = txt.search(r"and|on|with|product|is|(compl.)", '1.0', stopindex=END, regexp=True)
while pos != '':
while (txt.get(pos) != "") & (txt.get(pos) != " ") & (txt.get(pos) != "\n"):
txt.tag_add("whiteblue", pos)
pos = pos.__add__("+ 1 chars")
pos = txt.search(r"and|on|with|product|is|(compl.)", pos.__add__("+ 1 chars"), stopindex=END, regexp=True)
# Highlight specific genes
pos = txt.search("@", '1.0', stopindex=END)
while pos != '':
pos2 = pos.__add__("lineend")
if pos2 == '':
pos2 = END
color = "blueish"
txt.tag_add(color, pos.__add__("+ 1 chars"), pos2)
pos = txt.search("@", pos2, stopindex=END)
# Numbers, bp, etc (orange)
pos = txt.search(" L,", '1.0', stopindex=END)
while pos != '':
txt.tag_add("orangetxt", pos.__add__("+ 1 chars"))
pos = txt.search(" L,", pos.__add__("+ 1 chars"), stopindex=END)
pos = txt.search(r"\d", '1.0', stopindex=END, regexp=True)
while (pos != ''):
while (txt.get(pos.__add__("- 1 chars")) == "+") | (txt.get(pos.__add__("- 1 chars")) == " ") | (
("orangetxt" in txt.tag_names(pos.__add__(" - 1 chars"))) & (txt.get(pos) in "1234567890")):
txt.tag_add("orangetxt", pos)
txt.tag_remove("blueish", pos)
pos = pos.__add__("+ 1 chars")
pos = txt.search(r"\d", pos.__add__("+ 1 chars"), stopindex=END, regexp=True)
pos = txt.search("bp", '1.0', stopindex=END)
while pos != '':
pos2 = pos
pos = pos.__add__("+ 1 chars")
txt.tag_add("orangetxt", pos)
pos = pos.__add__("- 1 chars")
txt.tag_add("orangetxt", pos)
pos = pos.__add__("- 1 chars")
while not (util.isCrap(pos, txt)):
if txt.get(pos) in "1234567890":
txt.tag_add("orangetxt", pos)
pos = pos.__add__("- 1 chars")
else:
break
pos = txt.search(r"bp", pos2.__add__("+ 1 chars"), stopindex=END, regexp=True)
pos = txt.search(">", '1.0', stopindex=END)
while pos != '':
pos = pos.__add__("+ 1 chars")
color = util.seqColor(pos, txt)
while (txt.get(pos.__add__("+ 1 chars")) != txt.get(pos.__add__(" lineend"))):
if txt.get(pos) == " ":
color = "greygreen"
if not (txt.get(pos.__add__("+ 1 chars")) != txt.get(pos.__add__(" lineend"))):
pos = pos.__add__("+ 1 chars")
if (txt.get(pos) == "a") & (txt.get(pos.__add__("+ 1 chars")) == "n") & \
(txt.get(pos.__add__("+ 2 chars")) == "d") & (txt.get(pos.__add__("+ 3 chars")) == " "):
pos = pos.__add__("+ 4 chars")
# color = util.seqColor(pos, txt)
if (txt.get(pos) == "o") & (txt.get(pos.__add__("+ 1 chars")) == "n") & \
(txt.get(pos.__add__("+ 3 chars")) == " "):
pos = pos.__add__("+ 3 chars")
# color = util.seqColor(pos, txt)
else:
txt.tag_add(color, pos)
pos = pos.__add__("+ 1 chars")
if not util.isCrap(pos, txt):
txt.tag_add(color, pos)
pos = txt.search(">", pos.__add__("+ 1 chars"), stopindex=END)
for enzyme in enzymes:
txt.tag_config(enzyme.name, foreground=enzyme.color, underline=True)
txt.tag_config("_" + enzyme.name, foreground="black", background=enzyme.color)
pos = txt.search(enzyme.name, '1.0', stopindex=END, regexp=True)
while pos != '':
while not (util.isCrap(pos, txt)):
txt.tag_add(enzyme.name, pos)
pos = pos.__add__("+ 1 chars")
pos = txt.search(enzyme.name, pos.__add__("+ 1 chars"), stopindex=END, regexp=True)
regex = r"(?i)(" + enzyme.site + "|" + enzyme.siteRC + ").*"
# 'Degenerate' enzymes don't care about a specific middle part, only the outsides
if (enzyme.type == "Degenerate cutter") | ("(Type II" in enzyme.type) :
numN = 0
bit1=""
bit2=""
numX = 0
bit1RC=""
bit2RC=""
for l in enzyme.site :
if l == 'n' :
numN+=1
elif numN == 0 :
bit1+=l
else :
bit2+=l
for l in enzyme.siteRC:
if l == 'n':
numX += 1
elif numX == 0:
bit1RC += l
else:
bit2RC += l
regex = r"(?i)(" + "("+bit1+").{"+str(numN)+"}("+bit2+")" + "|" + "("+bit1RC+").{"+str(numX)+"}("+bit2RC+")" + ").*"
if (enzyme.type == "Degenerate cutter") :
numN = 0
bit1 = ""
bit2 = ""
numX = 0
bit1RC = ""
bit2RC = ""
for l in enzyme.site:
if l == 'n':
numN += 1
elif numN == 0:
bit1 += l
else:
bit2 += l
for l in enzyme.siteRC:
if l == 'n':
numX += 1
elif numX == 0:
bit1RC += l
else:
bit2RC += l
regex = r"(?i)(" + "(" + bit1 + ").{" + str(
numN) + "}(" + bit2 + ")" + "|" + "(" + bit1RC + ").{" + str(numX) + "}(" + bit2RC + ")" + ").*"
pos = txt.search(regex, '1.0', stopindex=END, regexp=True)
while pos != '':
for x in range(enzyme.cutOnCompl+enzyme.cutBefore):
txt.tag_add("_"+ enzyme.name, pos)
pos = pos.__add__("+ 1 chars")
pos = txt.search(regex, pos.__add__("+ 1 chars"), stopindex=END, regexp=True)
for color in colors:
txt.tag_config(color, foreground=color, underline=True)
#txt.tag_config("_" + enzyme.name, foreground="black", background=enzyme.color)
pos = txt.search(color, '1.0', stopindex=END, regexp=True)
while pos != '':
while not (util.isCrap(pos, txt)):
txt.tag_add(color, pos)
txt.tag_remove("blueish", pos)
pos = pos.__add__("+ 1 chars")
pos = txt.search(color, pos.__add__("+ 1 chars"), stopindex=END, regexp=True)
pos = txt.search("#", '1.0', stopindex=END)
while pos != '':
pos2 = pos.__add__("lineend")
if pos2 == '':
pos2 = END
for t in tags:
txt.tag_remove(t, pos, pos2)
color = "grey"
txt.tag_add(color, pos, pos2)
pos = txt.search("#", pos2, stopindex=END)
pos = txt.search("{", '1.0', stopindex=END)
while pos != '':
pos2 = txt.search("}", pos, stopindex=END).__add__("+ 1 chars")
if pos2 == '+ 1 chars':
pos2 = END
for t in tags:
txt.tag_remove(t, pos, pos2)
color = "grey"
txt.tag_add(color, pos, pos2)
pos = txt.search("{", pos2, stopindex=END)
pos = txt.search("*", '1.0', stopindex=END)
while pos != '':
pos2 = txt.search("*", pos, stopindex=END).__add__("+ 1 chars")
if pos2 == '+ 1 chars':
pos2 = END
for t in tags:
txt.tag_remove(t, pos, pos2)
color = "orange"
txt.tag_add(color, pos, pos2)
pos = txt.search("*", pos2, stopindex=END)
txt.tag_configure("sel", background=blue)
txt.tag_raise("sel")
util = Util
util.textStyle(util, editor)
# Inserts and parses a FASTA file
def insertFASTA(name):
fileStr = open(name).read()
namePos = fileStr.find("LOCUS") + 6
while Util.isCrapStr(Util, namePos, fileStr):
namePos += 1
seqName = Util.getVarNameStr(Util, namePos, fileStr, False)
sequence = ""
for l in fileStr[fileStr.find("ORIGIN")+7:] :
if l in "atcgATCG":
sequence += l.lower()
namePos = fileStr.find("FEATURES")
spot = 0
spotLabel = 0
i=0
while namePos < fileStr.__len__() :
complim = ""
while Util.isCrapStr(Util, namePos, fileStr) & (namePos < fileStr.__len__()):
namePos += 1
gene = Util.getVarNameStr(Util, namePos, fileStr, False)
print(fileStr[namePos-6])
if (fileStr[namePos-6] == '\n') :
if (fileStr[namePos] not in '1234567890'):
color = ""
if fileStr[spot:].find("fwdcolor=") > 0 :
color = Util.getVarNameStr(Util, fileStr[spot:].find("fwdcolor=")+9, fileStr[spot:], False)
spot += fileStr[spot:].find("fwdcolor=") + 9
colors.append(color)
else :
color = colors[i]
label = ""
if fileStr[spotLabel:].find("label=") > 0:
label = Util.getVarNameStr(Util, fileStr[spotLabel:].find("label=") + 6, fileStr[spotLabel:], True)
spotLabel+= fileStr[spotLabel:].find("label=") + 6
else:
label = gene
namePos += gene.__len__()
while Util.isCrapStr(Util, namePos, fileStr) & (namePos < fileStr.__len__()):
namePos += 1
fromPos = Util.getVarNameStr(Util, namePos, fileStr, False)
newPos = 0
if fromPos == "complement":
complim = "(compl.)"
newPos = 11
fromPos = Util.getVarNameStr(Util, (namePos+newPos), fileStr, False)
namePos += fromPos.__len__() + newPos
while Util.isCrapStr(Util, namePos, fileStr) & (namePos < fileStr.__len__()):
namePos += 1
toPos = Util.getVarNameStr(Util, namePos, fileStr, False)
space1 = ""
for l in range(26-label.__len__()) :
space1 += " "
space2 = ""
for l in range(10-fromPos.__len__()) :
space1 += " "
space3 = ""
for l in range(6-toPos.__len__()) :
space1 += " "
editor.insert(END, "\n@" + label + space1 + fromPos + space3 + space2 +" " + toPos + space3 + " " + color +" " + seqName + " #"+gene+" "+ complim)
namePos += gene.__len__()
i = (i + 1) % colors.__len__()
editor.insert(END, "\n>" + seqName + "\n")
editor.insert(END, sequence)
# The Enzyme class
class Enzyme:
name = ""
site = "" # 5'-3'
siteRC = "" # 3'-5' # the reverse compliment of the site
color = ""
cutBefore = 0 # cuts before this index on this strand
cutOnCompl = 0 # cuts before this index on the complimentary strand
stickyEnd = "" # the sticky end
reverseSticky = ""
type = ""
siteCut = ""
siteCut2 = ""
def get(self, str): # gets the Enzyme class from the name
for e in enzymes :
if str.__eq__(e.name) :
return e
return "null"
def digest(self, seq, instruct): # Digests a sequence - cuts and produces sticky ends at the specific restriction sites
sequence = seq.sequence
new_seq = str.lower(sequence)
for e in instruct:
print(e.name)
spot = new_seq.find(e.site)
spot += len(e.site)
new_seq = new_seq[
:spot - len(e.site)+e.cutOnCompl] + e.reverseSticky + " \n\n>" + seq.name + "\n " + e.stickyEnd + new_seq[spot-len(e.site)+e.cutBefore:]
return new_seq
def addNew(self, n, s, c, before, compl, t): # Adds a new Enzyme and appends it to enzymes[]
e = Enzyme()
e.site = s
e.name = n
e.siteRC = Util.rev_complement(Util, s)
e.color = c
e.cutBefore = before
e.cutOnCompl = compl
e.stickyEnd = Util.superscript(Util, s[before:compl])
e.reverseSticky = "{" + Util.superscript(Util, reverse(e.siteRC[e.site.__len__()-compl:e.site.__len__()-before])) + "}"
e.type = t
enzymes.append(e)
e.siteCut = e.site[:before]+"|"+e.site[before:]+" 3' {" + e.siteRC[:compl]+"|"+e.site[compl:]+"}"
e.siteCut2 = " "
def toHex(self, r, g, b): # Converts an RGB color to a hexcode
return '#%02x%02x%02x' % (r, g, b)
def __str__(self):
return self.name
def arrayStr(self, list):
str = ""
for e in list:
str += e.__str__() + ", "
return str
# Type II Restriction Endonucleases
#5' 4bp Overhang
Enzyme.addNew(Enzyme, "XhoI", "CTCGAG", Enzyme.toHex(Enzyme, 120, 140, 229), 5, 1, "3' 4bp overhang")
Enzyme.addNew(Enzyme, "NcoI", "CCATGG", Enzyme.toHex(Enzyme, 120, 100, 229), 5, 1, "3' 4bp overhang")
Enzyme.addNew(Enzyme, "EcoRI", "gaattc", Enzyme.toHex(Enzyme, 200, 240, 69), 1, 5, "5' 4bp overhang")
Enzyme.addNew(Enzyme, "EcoRI", "gaattc", Enzyme.toHex(Enzyme, 200, 240, 69), 1, 5, "5' 4bp overhang")
Enzyme.addNew(Enzyme, "SpeI", "actagt", Enzyme.toHex(Enzyme, 120, 120, 244), 1, 5, "5' 4bp overhang")
Enzyme.addNew(Enzyme, "BamHI", "ggatcc", Enzyme.toHex(Enzyme, 220, 120, 244), 1, 5, "5' 4bp overhang")
Enzyme.addNew(Enzyme, "XbaI", "tctaga", Enzyme.toHex(Enzyme, 100, 240, 69), 1, 5, "5' 4bp overhang")
Enzyme.addNew(Enzyme, "XbaI", "tctaga", Enzyme.toHex(Enzyme, 100, 240, 69), 1, 5, "5' 4bp overhang")
Enzyme.addNew(Enzyme, "BglII", "agatct", Enzyme.toHex(Enzyme, 60, 210, 150), 5, 1, "3' 4bp overhang")
#3' 4bp Overhang
Enzyme.addNew(Enzyme, "NotI", "gcggccgc", Enzyme.toHex(Enzyme, 100, 200, 69), 3, 7, "3' 4bp overhang")
#3' 4bp Overhang
Enzyme.addNew(Enzyme, "PstI", "ctgcag", Enzyme.toHex(Enzyme, 244, 89, 66), 5, 1, "3' 4bp overhang")
#5' 2bp Overhang
Enzyme.addNew(Enzyme, "NdeI", "catatg", Enzyme.toHex(Enzyme, 244, 89, 126), 2, 4, "5' 2bp overhang")
#3' 2bp Overhang
Enzyme.addNew(Enzyme, "PacI", "ttaattaa", Enzyme.toHex(Enzyme, 244, 189, 66), 5, 3, "3' 2bp overhang")
#Blunt cutters
Enzyme.addNew(Enzyme, "EcoRV", "gatatc", Enzyme.toHex(Enzyme, 244, 89, 0), 3, 3, "Blunt cutter")
Enzyme.addNew(Enzyme, "PvuII", "cagctg", Enzyme.toHex(Enzyme, 44, 209, 66), 3, 3, "Blunt cutter")
#Degenerate cutters
Enzyme.addNew(Enzyme, "XcmI", "ccannnnnnnnntgg", Enzyme.toHex(Enzyme, 44, 89, 166), 8, 7, "Degenerate cutter")
Enzyme.addNew(Enzyme, "AlwNI", "cagnnnctg", Enzyme.toHex(Enzyme, 24, 209, 66), 6, 3, "Degenerate cutter")
Enzyme.addNew(Enzyme, "SfiI", "ggccnnnnnggcc", Enzyme.toHex(Enzyme, 214, 89, 66), 8, 5, "Degenerate cutter")
#Enzyme.addNew(Enzyme, "FalI", "NNNNNNNNNNNNNNAAGNNNNNCTTNNNNNNNNNNNNNN", Enzyme.toHex(Enzyme, 66, 89, 244), 5, 3)
#Type IIS Restriction Endonucleases
Enzyme.addNew(Enzyme, "BsaI", "ggtctcnnnnn", Enzyme.toHex(Enzyme, 214, 189, 66), 4, 7, "(Type IIS) 5' 4bp overhang")
Enzyme.addNew(Enzyme, "BsmBI", "cgtctcnnnnn", Enzyme.toHex(Enzyme, 100, 140, 229), 7, 10, "(Type IIS) for GGR")
#Type IIG Restriction Endonucleases
Enzyme.addNew(Enzyme, "BseRI", "gaggagnnnnnnnnga", Enzyme.toHex(Enzyme, 30, 240, 189), 14, 2, "(Type IIG) 3' 2bp overhang")
# Loops indefinitely
def running():
i = 0
while True:
time.sleep(0.01)
i += 1
# updates text style every second
if (i % 100 == 0):
util.textStyle(util, editor)
util.updateColorToSelection(util, whatIs, whatIs2, whatIs3)
util.updateBpToSelection(util, label)
root.update_idletasks()
root.update()
# Shows the genes
def show_genes():
Gene.initGenes(Gene)
Util.geneStyle(Util)
editor.tag_remove('', '1.0', END)
# The Instruction class
class Instruction:
type = "" # PCR, ligation, transformation, PCA, or digestion
input1 = "" # which sequences are the reactants
input2 = ""
inputOn = "" # inputOn - for instructions with a sole input or for PCR, to specify what it is being
# done on, ie. 'pcr x and y on inputOn'
enzymes = [] # the list of enzymes used in the instruction
output = "" # the output sequence