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# Copyright 2000 by Katharine Lindner (Cayte).
# Copyright 2016 by Markus Piotrowski.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# The original SeqGui was written by Katharine Lindner (Cayte) in 2000 using
# the wxPython library for the GUI. It was rewritten by Markus Piotrowski in
# 2016 using tkinter and tkinter's themed widgets (ttk).
"""A small GUI tool to demonstrate some basic sequence operations.
SeqGui (sequence graphical user interface) is a little tool that allows
transcription, translation and back translation of a sequence that the
user can type or copy into a text field. For translation the user can select
from several codon tables which are implemented in Biopython.
It runs as a standalone application.
"""
from __future__ import print_function
from Bio.Seq import translate, transcribe, back_transcribe
from Bio.Data import CodonTable
try: # Python 2
import Tkinter as tk
import ttk
except ImportError: # Python 3
import tkinter as tk
import tkinter.ttk as ttk
main_window = tk.Tk()
main_window.title('Greetings from Biopython')
menue = tk.Menu(main_window)
menue_single = tk.Menu(menue, tearoff=0)
menue.add_cascade(menu=menue_single, label='File')
menue_single.add_command(label='About')
menue_single.add_separator()
menue_single.add_command(label='Exit', command=main_window.destroy)
main_window.config(menu=menue)
# Left panel with parameters
param_panel = ttk.Frame(main_window, relief=tk.GROOVE, padding=5)
codon_panel = ttk.LabelFrame(param_panel, text='Codon Tables')
codon_scroller = ttk.Scrollbar(codon_panel, orient=tk.VERTICAL)
codon_list = tk.Listbox(codon_panel, height=5, width=25,
yscrollcommand=codon_scroller.set)
# Import actual codon tables from Biopython and sort alphabetically
codon_table_list = sorted([table.names[0] for n, table in
CodonTable.generic_by_id.items()])
# 'Standard' table should be first in the list
del(codon_table_list[codon_table_list.index('Standard')])
codon_table_list.insert(0, 'Standard')
for codon_table in codon_table_list:
codon_list.insert(tk.END, codon_table)
codon_list.selection_set(0)
codon_list.configure(exportselection=False)
codon_scroller.config(command=codon_list.yview)
# Radiobuttons are more appropiate than another listbox here:
transform_panel = ttk.LabelFrame(param_panel, text='Transformation')
transform_var = tk.StringVar()
transform_transcribe = ttk.Radiobutton(transform_panel, text='Transcribe',
variable=transform_var,
value='transcribe')
transform_translate = ttk.Radiobutton(transform_panel, text='Translate',
variable=transform_var,
value='translate')
transform_backtranscribe = ttk.Radiobutton(transform_panel,
text='Back transcribe',
variable=transform_var,
value='back transcribe')
transform_translate.invoke()
# Right panel with sequence in- and output
seq_panel = ttk.Frame(main_window, relief=tk.GROOVE, padding=5)
input_panel = ttk.LabelFrame(seq_panel, text='Original Sequence')
input_scroller = ttk.Scrollbar(input_panel, orient=tk.VERTICAL)
input_text = tk.Text(input_panel, width=39, height=5,
yscrollcommand=input_scroller.set)
input_scroller.config(command=input_text.yview)
output_panel = ttk.LabelFrame(seq_panel, text='Transformed Sequence')
output_scroller = ttk.Scrollbar(output_panel, orient=tk.VERTICAL)
output_text = tk.Text(output_panel, width=39, height=5,
yscrollcommand=output_scroller.set)
output_scroller.config(command=output_text.yview)
# Buttons
apply_button = ttk.Button(seq_panel, text='Apply')
clear_button = ttk.Button(seq_panel, text='Clear')
close_button = ttk.Button(seq_panel, text='Close', command=main_window.destroy)
# Statusbar
statustext = tk.StringVar()
statusbar = ttk.Label(main_window, textvariable=statustext, relief=tk.GROOVE,
padding=5)
statustext.set('This is the statusbar')
sizegrip = ttk.Sizegrip(statusbar)
# Event methods
def clear_output():
"""Clear the output window."""
input_text.delete(1.0, tk.END)
output_text.delete(1.0, tk.END)
return
def apply_operation():
"""Do the selected operation."""
codon_table = codon_list.get(codon_list.curselection())
print('Code: {}'.format(codon_table))
seq = ''.join(input_text.get(1.0, tk.END).split())
print('Input sequence: {}'.format(seq))
operation = transform_var.get()
print('Operation: {}'.format(operation))
if operation == 'transcribe':
result = transcribe(seq)
elif operation == 'translate':
result = translate(seq, table=codon_table, to_stop=True)
elif operation == 'back transcribe':
result = back_transcribe(seq)
else:
result = ''
output_text.delete(1.0, tk.END)
output_text.insert(tk.END, result)
print('Result: {}'.format(result))
return
def set_statusbar(event):
"""Show statusbar comments from menu selection."""
index = main_window.call(event.widget, "index", "active")
if index == 0:
statustext.set('More information about this program')
elif index == 2:
statustext.set('Terminate the program')
else:
statustext.set('This is the statusbar')
return
# Set commands and bind events
menue_single.bind('<<MenuSelect>>', set_statusbar)
apply_button.config(command=apply_operation)
clear_button.config(command=clear_output)
# Build GUI
statusbar.pack(side=tk.BOTTOM, padx=1, fill=tk.X)
sizegrip.pack(side=tk.RIGHT, padx=3, pady=4)
param_panel.pack(side=tk.LEFT, anchor=tk.N, padx=5, pady=10, fill=tk.Y)
codon_panel.pack(fill=tk.Y, expand=True)
codon_scroller.pack(side=tk.RIGHT, fill=tk.Y)
codon_list.pack(fill=tk.Y, expand=True)
transform_panel.pack(pady=10, fill=tk.X)
transform_transcribe.pack(anchor=tk.W)
transform_translate.pack(anchor=tk.W)
transform_backtranscribe.pack(anchor=tk.W)
seq_panel.pack(anchor=tk.N, padx=5, pady=10, fill=tk.BOTH, expand=True)
input_panel.pack(fill=tk.BOTH, expand=True)
input_scroller.pack(side=tk.RIGHT, fill=tk.Y)
input_text.pack(fill=tk.BOTH, expand=True)
output_panel.pack(pady=10, fill=tk.BOTH, expand=True)
output_scroller.pack(side=tk.RIGHT, fill=tk.Y)
output_text.pack(fill=tk.BOTH, expand=True)
apply_button.pack(side=tk.LEFT)
clear_button.pack(side=tk.LEFT, padx=10)
close_button.pack(side=tk.LEFT)
main_window.mainloop()
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