Primer Design Tool:引物PCR设计-开源

""" Copyright (C) 2010-2012 Victor Khangulov - Johns Hopkins University This file is part of Primer Design Tool. Primer Design Tool is a free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/> Title: Primer Design Tool GUI File: dialog.py Description: This file is the GUI for the Primer Design Tool. This file contains the following classes: MutEntry - Object for user added mutation. BaseDialog - Class for the base dialog. The constructor allows user to specify a variable number of section (or frames) StdDialog - This is a class for the dialog with Quit, Next and Back button. It inherits from the BaseDialog SeqDialog - This is a sequence dialog (window #1). In this dialog, the user is required to enter their initials, date and select background ID. If the background is not available, the user can add a new background by loading a new DNA sequence. Next, user is able to add current mutations and new mutations. PrimerDialog- Primer dialog (Window #2). Display starting primer with new mutations and an overhang. Display DNA sequence 30 bp up and downstream of the starting primer. Do some simple calculations about Tm, #bp, GC content, residues covered. Allow user to choose alternate codons for the mutations that were specified, and allow them to enter additional bp on either side of the primer. Usage: execute PrimerDesigner.py file to run program Website: https://sourceforge.net/apps/mediawiki/primer-design/index.php?title=Main_Page Created: 2010.Nov.04 VK Repository path: $HeadURL$ Last committed: $Revision$ Last changed by: $Author$ Last changed date: $Date$ ID: $Id$ """ # Import python standard modules import sys, os # Import modules try: from Tkinter import * import FileDialog, tkMessageBox, Dialog, tkFileDialog except ImportError: print "TK required!" sys.exit() from tkModule import * from utils import * from PrimerDesigner import Mutation from datetime import datetime from string import * from math import ceil class AutoScrollbar(Scrollbar): # a scrollbar that hides itself if it's not needed. only # works if you use the grid geometry manager. def set(self, lo, hi): if float(lo) <= 0.0 and float(hi) >= 1.0: # grid_remove is currently missing from Tkinter! self.tk.call("grid", "remove", self) else: self.grid() Scrollbar.set(self, lo, hi) def pack(self, **kw): raise TclError, "cannot use pack with this widget" def place(self, **kw): raise TclError, "cannot use place with this widget" class MutEntry: """ Class to create object each time the user adds another mutation. """ def __init__(self, master, mut_id): """ Initialize mutation entry. This will create a separate frame for each mutation and the required entry boxes.""" # Create the entry box for the mutation self.frame = Frame(master) self.label = StandardLabel(self.frame, \ label_text="Mutation #%d:"%mut_id) self.res1 = EntryBox(self.frame,entry_type=str, tag="res1-%d"%mut_id,\ entry_width=1, allow_blank=True) self.res1.config(width=2) self.pos = EntryBox(self.frame, entry_type=int,tag="res_pos-%d"%mut_id,\ entry_width=3, allow_blank=True) self.pos.config(width=4) self.res2 = EntryBox(self.frame, entry_type=str, tag="res2-%d"%mut_id,\ entry_width=1,allow_blank=True) self.res2.config(width=2) self.label.grid(row=0,column=0,sticky=W) self.res1.grid(row=0,column=1,sticky=W) self.pos.grid(row=0,column=2,sticky=W) self.res2.grid(row=0,column=3,sticky=W) self.frame.pack() def get_mutation(self): """ Return a list containing the mutation. For now, just add a place- holder 'XXX' for the new codon and for the old codon """ # If index had not been entered, then set it to some arbitrary number if self.pos.get() == None: index = None else: index = int(self.pos.get()) return [str(self.res1.get()).upper(),index,\ str(self.res2.get()).upper(), "XXX", "XXX"] class BaseDialog(object): """ Class for the base dialog. The constructor allows user to specify a variable number of section (or frames) """ def __init__(self, master, nframes=1): """ Constructor. User can set the optional nframes argumet to set the number of frames to be pre-created. """ self.master = master vscrollbar = AutoScrollbar(master) vscrollbar.grid(row=0, column=1, sticky=N+S) hscrollbar = AutoScrollbar(master, orient=HORIZONTAL) hscrollbar.grid(row=1, column=0, sticky=E+W) self.canvas = Canvas(master, yscrollcommand=vscrollbar.set, xscrollcommand=hscrollbar.set) self.canvas.grid(row=0, column=0, sticky=N+S+E+W) vscrollbar.config(command=self.canvas.yview) hscrollbar.config(command=self.canvas.xview) # make the canvas expandable master.grid_rowconfigure(0, weight=1) master.grid_columnconfigure(0, weight=1) # # create canvas contents self.mframe = Frame(self.canvas, border=5) self.mframe.grid(row=0, column=0) self.mframe.rowconfigure(0, weight=1) self.mframe.columnconfigure(0, weight=1) self.frames = [] # Create frames j = 0 for i in range(nframes): self.frames.append(Frame(self.mframe, border=5)) self.frames[i].grid(row=j,column=0,sticky=EW) self.frames[i].columnconfigure(0, weight=1) j += 1 self.div = Divider(self.mframe,arrangement="h") self.div.grid(row=j,column=0,sticky=EW) j += 1 # Bottom button pane self.bpane = Frame(self.mframe, border=5) self.bpane.grid(row=j,column=0,sticky=EW) self.bpane.columnconfigure(0, weight=1) self.bpane.columnconfigure(1, weight=1) self.bpane.columnconfigure(2, weight=1) #rows = 5 #for i in range(0,rows): # for j in range(0,10): # button = Button(self.bpane, padx=7, pady=7, text="[%d,%d]" % (i,j)) # button.grid(row=i, column=j, sticky='news') def update_canvas(self):