-
Notifications
You must be signed in to change notification settings - Fork 5
/
run_dimple_gui.py
312 lines (265 loc) · 15.1 KB
/
run_dimple_gui.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
# RUN DIMPLE
# script for GUI
from DIMPLE.DIMPLE import align_genevariation, print_all, post_qc, addgene, DIMPLE, generate_DMS_fragments, switch_fragmentsize
from DIMPLE.utilities import parse_custom_mutations
from Bio.Seq import Seq
import tkinter as tk
from tkinter import filedialog
from tkinter import messagebox
import ast
from io import StringIO
def run():
if not any([app.delete.get(), app.insert.get(), app.include_substitutions.get(), app.dis.get()]):
messagebox.showerror('Python Error', 'Error: You must select a mutation type.')
raise ValueError('You must select a mutation type')
if app.wDir is None:
app.wDir = app.geneFile.rsplit('/', 1)[0]+'/'
if any([x not in ['A', 'C', 'G', 'T', 'a', 'c', 'g', 't'] for x in app.handle.get()]):
raise ValueError('Genetic handle contains non nucleic bases')
DIMPLE.synth_len = int(app.oligoLen.get())
overlapL = int(app.overlap.get())
overlapR = int(app.overlap.get())
if app.delete.get():
overlapR = max([int(x) for x in app.deletions.get().split(',')]) + overlapR - 3
if app.fragmentLen.get() != 'auto':
DIMPLE.maxfrag = int(app.fragmentLen.get())
else:
DIMPLE.maxfrag = int(app.oligoLen.get()) - 62 - overlapL - overlapR # 62 allows for cutsites and barcodes
#adjust primer primerBuffer
DIMPLE.primerBuffer += overlapL
if app.codon_usage == 'ecoli':
DIMPLE.usage = {
'TTT': 0.58, 'TTC': 0.42, 'TTA': 0.14, 'TTG': 0.13, 'TAT': 0.59, 'TAC': 0.41, 'TAA': 0.61, 'TAG': 0.09,
'CTT': 0.12, 'CTC': 0.1, 'CTA': 0.04, 'CTG': 0.47, 'CAT': 0.57, 'CAC': 0.43, 'CAA': 0.34, 'CAG': 0.66,
'ATT': 0.49, 'ATC': 0.39, 'ATA': 0.11, 'ATG': 1, 'AAT': 0.49, 'AAC': 0.51, 'AAA': 0.74, 'AAG': 0.26,
'GTT': 0.28, 'GTC': 0.2, 'GTA': 0.17, 'GTG': 0.35, 'GAT': 0.63, 'GAC': 0.37, 'GAA': 0.68, 'GAG': 0.32,
'TCT': 0.17, 'TCC': 0.15, 'TCA': 0.14, 'TCG': 0.14, 'TGT': 0.46, 'TGC': 0.54, 'TGA': 0.3, 'TGG': 1,
'CCT': 0.18, 'CCC': 0.13, 'CCA': 0.2, 'CCG': 0.49, 'CGT': 0.36, 'CGC': 0.36, 'CGA': 0.07, 'CGG': 0.11,
'ACT': 0.19, 'ACC': 0.4, 'ACA': 0.17, 'ACG': 0.25, 'AGT': 0.16, 'AGC': 0.25, 'AGA': 0.07, 'AGG': 0.04,
'GCT': 0.18, 'GCC': 0.26, 'GCA': 0.23, 'GCG': 0.33, 'GGT': 0.35, 'GGC': 0.37, 'GGA': 0.13, 'GGG': 0.15
} # E.coli codon usage table
elif app.codon_usage == 'human':
DIMPLE.usage = {
'TTT': 0.45, 'TTC': 0.55, 'TTA': 0.07, 'TTG': 0.13, 'TAT': 0.43, 'TAC': 0.57, 'TAA': 0.28, 'TAG': 0.2,
'CTT': 0.13, 'CTC': 0.2, 'CTA': 0.07, 'CTG': 0.41, 'CAT': 0.41, 'CAC': 0.59, 'CAA': 0.25, 'CAG': 0.75,
'ATT': 0.36, 'ATC': 0.48, 'ATA': 0.16, 'ATG': 1, 'AAT': 0.46, 'AAC': 0.54, 'AAA': 0.42, 'AAG': 0.58,
'GTT': 0.18, 'GTC': 0.24, 'GTA': 0.11, 'GTG': 0.47, 'GAT': 0.46, 'GAC': 0.54, 'GAA': 0.42, 'GAG': 0.58,
'TCT': 0.18, 'TCC': 0.22, 'TCA': 0.15, 'TCG': 0.06, 'TGT': 0.45, 'TGC': 0.55, 'TGA': 0.52, 'TGG': 1,
'CCT': 0.28, 'CCC': 0.33, 'CCA': 0.27, 'CCG': 0.11, 'CGT': 0.08, 'CGC': 0.19, 'CGA': 0.11, 'CGG': 0.21,
'ACT': 0.24, 'ACC': 0.36, 'ACA': 0.28, 'ACG': 0.12, 'AGT': 0.15, 'AGC': 0.24, 'AGA': 0.2, 'AGG': 0.2,
'GCT': 0.26, 'GCC': 0.4, 'GCA': 0.23, 'GCG': 0.11, 'GGT': 0.16, 'GGC': 0.34, 'GGA': 0.25, 'GGG': 0.25
}
else:
DIMPLE.usage = app.codon_usage
DIMPLE.barcodeF = DIMPLE.barcodeF[int(app.barcode_start.get()):]
DIMPLE.barcodeR = DIMPLE.barcodeR[int(app.barcode_start.get()):]
tmp_cutsite = app.restriction_sequence.get().split('(')
DIMPLE.cutsite = Seq(tmp_cutsite[0])
DIMPLE.cutsite_buffer = Seq(tmp_cutsite[1].split(')')[0])
tmp_overhang = tmp_cutsite[1].split(')')[1].split('/')
DIMPLE.cutsite_overhang = int(tmp_overhang[1]) - int(tmp_overhang[0])
DIMPLE.avoid_sequence = [Seq(x) for x in app.avoid_sequence.get().split(',')]
DIMPLE.aminoacids = app.substitutions.get().split(',')
DIMPLE.stop_codon = app.stop.get()
DIMPLE.dms = app.include_substitutions.get()
DIMPLE.make_double = app.make_double.get()
DIMPLE.handle = app.handle.get()
DIMPLE.doublefrag = app.doublefrag
DIMPLE.gene_primerTm = (int(app.melting_temp_low.get()), int(app.melting_temp_high.get()))
DIMPLE.maximize_nucleotide_change = app.max_mutations.get()
OLS = addgene(app.geneFile)
if app.avoid_breaksites.get():
OLS[0].problemsites = set(int(x) for x in app.custom_mutations.keys())
# add extras
if app.avoid_others_list.get() != '':
OLS[0].problemsites.update([int(x) for x in app.avoid_others_list.get().split(',')])
for i in range(len(OLS[0].breaksites)):
switch_fragmentsize(OLS[0], 1, OLS)
if app.matchSequences.get() == 'match':
align_genevariation(OLS)
if app.delete.get() == 0:
deletions = False
else:
deletions = [int(x) for x in app.deletions.get().split(',')]
if app.insert.get() == 0:
insertions = False
else:
insertions = app.insertions.get().split(',')
generate_DMS_fragments(OLS, overlapL, overlapR, app.synonymous.get(), app.custom_mutations, app.include_substitutions.get(), insertions, deletions, app.dis.get(), app.wDir)
post_qc(OLS)
print_all(OLS, app.wDir)
class Application(tk.Frame):
def __init__(self, master=None):
super().__init__(master)
self.master = master
self.pack()
self.create_widgets()
def create_widgets(self):
self.winfo_toplevel().title("DIMPLE Deep Indel Missense Programmable Library Engineering")
self.matchSequences = tk.IntVar()
self.mutationType = tk.IntVar()
self.usage = tk.IntVar()
self.include_substitutions = tk.IntVar()
self.delete = tk.IntVar()
self.insert = tk.IntVar()
self.stop = tk.IntVar()
self.synonymous = tk.IntVar()
self.dis = tk.IntVar()
self.make_double = tk.IntVar()
self.custom_mutations = {}
self.doublefrag = tk.IntVar()
self.avoid_breaksites = tk.IntVar()
self.max_mutations = tk.IntVar()
self.wDir_file = tk.Button(self, text='Working Directory', command=self.browse_wDir)
self.wDir_file.pack()
self.wDir = None
self.gene_file = tk.Button(self, text='Target Gene File', command=self.browse_gene)
self.gene_file.pack()
self.geneFile = None
tk.Label(self, text='Oligo Length').pack()
self.oligoLen = tk.Entry(self, textvariable=tk.StringVar(self, '250'))
self.oligoLen.pack()
tk.Label(self, text='Fragment Length').pack()
self.fragmentLen = tk.Entry(self, textvariable=tk.StringVar(self, 'auto'))
self.fragmentLen.pack()
tk.Label(self, text='Fragment Overlap (This will change if deletions are selected)').pack()
self.overlap = tk.Entry(self, textvariable=tk.StringVar(self, '4'))
self.overlap.pack()
tk.Label(self, text='Barcode Start position (3000 total available)').pack()
self.barcode_start = tk.Entry(self, textvariable=tk.StringVar(self, '0'))
self.barcode_start.pack()
tk.Label(self, text='Melting Temperature for Gene Primers').pack()
self.melting_temp_low = tk.Entry(self, textvariable=tk.StringVar(self, '58'))
self.melting_temp_low.pack()
self.melting_temp_high = tk.Entry(self, textvariable=tk.StringVar(self, '62'))
self.melting_temp_high.pack()
tk.Label(self, text='Type IIS restriction sequence (Do not use N)').pack()
self.restriction_sequence = tk.Entry(self, textvariable=tk.StringVar(self, 'CGTCTC(G)1/5'))
self.restriction_sequence.pack()
tk.Label(self, text='Sequences to avoid').pack()
self.avoid_sequence = tk.Entry(self, width=50, textvariable=tk.StringVar(self, 'CGTCTC, GGTCTC'))
self.avoid_sequence.pack()
self.stop_codon = tk.Checkbutton(self, text="Include Stop Codons", variable=self.stop)
self.stop_codon.pack()
self.synonymous_check = tk.Checkbutton(self, text="Include Synonymous Mutations", variable=self.synonymous)
self.synonymous_check.pack()
self.doublefrag_check = tk.Checkbutton(self, text="Double Fragments per Oligo", variable=self.doublefrag)
self.doublefrag_check.pack()
self.codon_usage = 'human'
self.custom_codons = {
'TTT': 0.45, 'TTC': 0.55, 'TTA': 0.07, 'TTG': 0.13, 'TAT': 0.43, 'TAC': 0.57, 'TAA': 0.28, 'TAG': 0.2,
'CTT': 0.13, 'CTC': 0.2, 'CTA': 0.07, 'CTG': 0.41, 'CAT': 0.41, 'CAC': 0.59, 'CAA': 0.25, 'CAG': 0.75,
'ATT': 0.36, 'ATC': 0.48, 'ATA': 0.16, 'ATG': 1, 'AAT': 0.46, 'AAC': 0.54, 'AAA': 0.42, 'AAG': 0.58,
'GTT': 0.18, 'GTC': 0.24, 'GTA': 0.11, 'GTG': 0.47, 'GAT': 0.46, 'GAC': 0.54, 'GAA': 0.42, 'GAG': 0.58,
'TCT': 0.18, 'TCC': 0.22, 'TCA': 0.15, 'TCG': 0.06, 'TGT': 0.45, 'TGC': 0.55, 'TGA': 0.52, 'TGG': 1,
'CCT': 0.28, 'CCC': 0.33, 'CCA': 0.27, 'CCG': 0.11, 'CGT': 0.08, 'CGC': 0.19, 'CGA': 0.11, 'CGG': 0.21,
'ACT': 0.24, 'ACC': 0.36, 'ACA': 0.28, 'ACG': 0.12, 'AGT': 0.15, 'AGC': 0.24, 'AGA': 0.2, 'AGG': 0.2,
'GCT': 0.26, 'GCC': 0.4, 'GCA': 0.23, 'GCG': 0.11, 'GGT': 0.16, 'GGC': 0.34, 'GGA': 0.25, 'GGG': 0.25
}
def openNewWindow():
newWindow = tk.Toplevel(self)
newWindow.title("Custom Codon Usage")
newWindow.geometry("900x400")
custom_codon = tk.Text(newWindow, width=750, height=400, wrap=tk.WORD)
custom_codon.pack()
# if self.codon_usage is not a dictionary then set it to self.custom_codons
if type(self.codon_usage) is not dict:
self.codon_usage = self.custom_codons
s = StringIO()
print(self.codon_usage, file=s)
custom_codon.insert(tk.END, s.getvalue())
def on_closing():
# set codon usage
self.codon_usage = ast.literal_eval(custom_codon.get("1.0", 'end-1c').strip('\n'))
newWindow.destroy()
newWindow.protocol("WM_DELETE_WINDOW", on_closing)
def ecoli_ON():
self.codon_usage = 'ecoli'
def human_ON():
self.codon_usage = 'human'
tk.Label(self, text='Codon Usage', font="helvetica 12 underline").pack(pady=5)
self.ecoli_check = tk.Radiobutton(self, text="E. coli", variable=self.usage, value=1, command=ecoli_ON)
self.ecoli_check.pack()
self.human_check = tk.Radiobutton(self, text="Human", variable=self.usage, value=0, command=human_ON)
self.human_check.pack()
self.custom_codon_button = tk.Button(self, text="Custom Codon Usage", command=openNewWindow)
self.custom_codon_button.pack()
tk.Label(self, text='Select Mutations', font="helvetica 12 underline").pack(pady=5)
self.include_dis = tk.Checkbutton(self, text='Domain Insertion Scan', variable=self.dis)
self.include_dis.pack()
self.handle = tk.Entry(self, width=50, textvariable=tk.StringVar(self, 'AGCGGGAGACCGGGGTCTCTGAGC'))
self.handle.pack()
self.delete_check = tk.Checkbutton(self, text="List of Deletions", variable=self.delete)
self.delete_check.pack()
self.delete_check.deselect()
self.deletions = tk.Entry(self, width=50, textvariable=tk.StringVar(self, '3,6'))
self.deletions.pack()
self.insert_check = tk.Checkbutton(self, text="List of Insertions", variable=self.insert)
self.insert_check.pack()
self.insert_check.deselect()
self.insertions = tk.Entry(self, width=50, textvariable=tk.StringVar(self, 'GGG,GGGGGG'))
self.insertions.pack()
self.include_sub_check = tk.Checkbutton(self, text='Deep Mutational Scan', variable=self.include_substitutions)
self.include_sub_check.pack()
self.include_sub_check.deselect()
self.max_mut = tk.Checkbutton(self, text='Maximize Nucleotide Change (2 or more)', variable=self.max_mutations)
self.max_mut.pack()
self.max_mut.deselect()
self.substitutions = tk.Entry(self, width=80, textvariable=tk.StringVar(self, "Cys,Asp,Ser,Gln,Met,Asn,Pro,Lys,Thr,Phe,Ala,Gly,Ile,Leu,His,Arg,Trp,Val,Glu,Tyr"))
self.substitutions.pack()
self.double_it = tk.Checkbutton(self, text='Make Double Mutations (Warning: Limit number of mutations)', variable=self.make_double)
self.double_it.pack()
self.double_it.deselect()
self.custom_mutations_button = tk.Button(self, text="Custom Mutations", command=self.custom_mutations_input)
self.custom_mutations_button.pack(pady=10)
self.avoid_custom = tk.Checkbutton(self, text='Avoid breaksites in Custom Mutations', variable=self.avoid_breaksites)
self.avoid_custom.pack()
tk.Label(self, text='Comma separated AA positions:').pack()
self.avoid_others_list = tk.Entry(self, width=60, textvariable=tk.StringVar(self, ""))
self.avoid_others_list.pack()
#self.matchSequences_check = tk.Checkbutton(self, text='Match Sequences', variable=self.matchSequences)
#self.matchSequences_check.pack()
self.run = tk.Button(self, text='Run DIMPLE', command=run).pack(pady=10)
self.output = tk.Text(self, height=5, width=60).pack()
def browse_wDir(self):
self.wDir = filedialog.askdirectory(title="Select a File")
if self.wDir != '':
self.wDir_file.config(bg='green', activebackground='green', relief=tk.SUNKEN)
else:
self.wDir = None
def browse_gene(self):
self.geneFile = filedialog.askopenfilename(title="Select a File")
if self.geneFile != '':
self.gene_file.config(bg='green', activebackground='green', relief=tk.SUNKEN)
else:
self.geneFile = None
# create a function to input custom mutations
def custom_mutations_input(self):
# create a new window
newWindow = tk.Toplevel(self)
newWindow.title("Custom Mutations (close window when finished)")
newWindow.geometry('700x1000')
# create a text box for custom mutations
custom_mutations_window = tk.Text(newWindow, height=50, width=80)
custom_mutations_window.pack()
# example mutations
if self.custom_mutations == {}:
custom_mutations_window.insert(tk.END, "Positions:Mutations\n1-10:All\n11-20:A,C,D,E,F,G,H,I,K,L\n33:A,C")
else:
custom_mutations_window.insert(tk.END, "Positions:Mutations\n")
for key, value in self.custom_mutations.items():
custom_mutations_window.insert(tk.END, str(key)+':'+value+'\n')
# create a button to set custom mutations
def on_closing():
# set custom mutations
mutation_text = custom_mutations_window.get("1.0", 'end-1c').strip().split('\n')
self.custom_mutations = parse_custom_mutations(mutation_text[1:])
newWindow.destroy()
newWindow.protocol("WM_DELETE_WINDOW", on_closing)
self.custom_mutations_button.config(bg='green', activebackground='green', relief=tk.SUNKEN)
self.include_substitutions.set(1)
if __name__ == "__main__":
root = tk.Tk()
root.geometry('700x1100')
app = Application(master=root)
app.mainloop()