diff --git a/blastGUI.py b/blastGUI.py new file mode 100644 index 0000000..eaa1ef7 --- /dev/null +++ b/blastGUI.py @@ -0,0 +1,272 @@ +#!/usr/bin/env python +# -*- coding:utf-8 -*- +# Author：Wu Qing +# E-mail: cipn@qq.com + +import os +import re +import subprocess +from tkinter import * +from tkinter.font import Font +from tkinter.ttk import * +from tkinter.messagebox import * +import tkinter.filedialog +import tkinter.simpledialog +from tkinter.ttk import Style +import shutil + + +def make_db(): + def make_db_button_cmd(): + if fndb == '': + return showinfo(title='warning', message='The build database file is not selected!') + if mkdb_type.get() != 'Nucleic acid sequence' and mkdb_type.get() != 'Protein sequence': + return showinfo(title='warning', message='The database type is not selected!') + if db_name_input.get() == '': + return showinfo(title='warning', message='Database name is not set!') + if mkdb_type.get() == 'Nucleic acid sequence': + t = 'nucl' + if mkdb_type.get() == 'Protein sequence': + t = 'prot' + n = db_name_input.get() + p = subprocess.Popen( + "makeblastdb -parse_seqids -in " + fndb + " -dbtype " + t + " -title " + n + " -out " + n, + shell=True, stdout=subprocess.PIPE) + p.wait() + out = p.stdout.readlines() + if p.returncode == 0: + showinfo(title="info", message="Database created successfully!") + makedb_state.delete(0.0, END) + for line in out: + makedb_state.insert("insert", line) + else: + showinfo(title="info", message="Database creation failed!") + + def select_fadb_button_cmd(): + global fndb + fndb = tkinter.filedialog.askopenfilename() + make_db_label.config(text="The files you selected:\n" + fndb) + + def mkdb_instruction(): + makedb_state.insert('1.0', "1. Click select file button to select FASTA file \n\n2. Select database type \n\ + \n3. Enter the name of the database (no Spaces)\n\ + \n4. Click create database button to start database building \n\ + \n5.After the database construction is completed, please restart this program to refresh the database list") + + dbwindow = Tk() + dbwindow.title('Create database') + dbwindow.geometry('600x400') + + mkdb_typeList = ['Nucleic acid sequence', 'Protein sequence', ] + mkdb_type = Combobox(dbwindow, text='Nucleic acid sequence', values=mkdb_typeList, font=('', 13)) + mkdb_type.place(relx=0.394, rely=0.192, relwidth=0.251) + + makedb_stateFont = Font(font=('', 13)) + makedb_state = Text(dbwindow, font=makedb_stateFont) + makedb_state.place(relx=0.041, rely=0.505, relwidth=0.915, relheight=0.435) + mkdb_instruction() + + style.configure('Tmake_db_button.TButton', font=('', 13)) + make_db_button = Button(dbwindow, text='Create database', command=make_db_button_cmd, style='Tmake_db_button.TButton') + make_db_button.place(relx=0.705, rely=0.216, relwidth=0.251, relheight=0.219) + + db_name_inputVar = StringVar(value='db') + db_name_input = Entry(dbwindow, textvariable=db_name_inputVar, font=('', 13)) + db_name_input.place(relx=0.394, rely=0.336, relwidth=0.251, relheight=0.099) + + style.configure('Tselect_fadb_button.TButton', font=('', 13)) + select_fadb_button = Button(dbwindow, text='Select file', command=select_fadb_button_cmd, style='Tselect_fadb_button.TButton') + select_fadb_button.place(relx=0.705, rely=0.048, relwidth=0.251, relheight=0.123) + + style.configure('Tdb_type_label.TLabel', anchor='w', font=('', 13)) + db_type_label = Label(dbwindow, text='Select database type', style='Tdb_type_label.TLabel') + db_type_label.place(relx=0.041, rely=0.192, relwidth=0.272, relheight=0.099) + + style.configure('Tdb_name.TLabel', anchor='w', font=('', 13)) + db_name = Label(dbwindow, text='Set database name', style='Tdb_name.TLabel') + db_name.place(relx=0.041, rely=0.336, relwidth=0.272, relheight=0.099) + + style.configure('Tmake_db_label.TLabel', anchor='center', font=('', 13)) + make_db_label = Label(dbwindow, text='You did not select any files', style='Tmake_db_label.TLabel') + make_db_label.place(relx=0.041, rely=0.048, relwidth=0.602, relheight=0.105) + + dbwindow.mainloop() + + +def get_fasta(): + input = fa_input.get() + tmp = ''.join(re.findall(r'[A-Za-z]', input)) + if tmp == '': + showinfo(title='warning', message='Please enter the correct sequence') + return 1 + else: + #tmp = str.upper(tmp) + with open("tmp.txt", "w+") as f: + f.write(tmp) + return 0 + + + +# get database name list +def get_db_name(): + namelist = [] + for fn in os.listdir(os.getcwd()): + if os.path.splitext(fn)[1] == '.phr' or os.path.splitext(fn)[1] == '.nhr': + fn = os.path.splitext(fn)[0] + namelist.append(fn) + return namelist + + +# blast process +def star(): + fnfa_stat = "The files you selected:" + fnfa + fain_stat = fa_input.get() + + if fnfa_stat == fain_stat: + fa = fnfa + else: + fa = 'tmp.txt' + + b = subprocess.Popen(blast_type.get() + " -out result.txt -query " + fa + " -outfmt " + outfmt_input.get() + + " -evalue " + evalue.get() + " -db " + db_type.get() + ' -num_threads ' + threat_input.get(), + shell=True, stdout=subprocess.PIPE) + b.wait() + + if b.returncode == 0: + result_output.delete(0.0, END) + with open("result.txt", "r") as result: + for line in result: + result_output.insert('insert', line) + else: + showinfo(title='warning', message='Wrong alignment!\nPlease make sure the parameters are set correctly!') + + +def star_blast_cmd(): + try: + os.remove((os.path.join(os.getcwd(), 'tmp.txt'))) + os.remove((os.path.join(os.getcwd(), 'result.txt'))) + finally: + if get_fasta() == 1: + return 1 + if get_fasta() == 0: + star() + return 0 + + +def select_fa_button_Cmd(): + global fnfa + fnfa = tkinter.filedialog.askopenfilename() + fa_input.delete(0, END) + if fnfa != '': + fa_input.insert(END, "The files you selected:" + fnfa) + else: + fa_input.insert(END, "Enter a sequence here or select a sequence file:") + pass + + + +def about_cmd(): + showinfo(title='Abount', message='BlstaGUI\n\nAuthor：Wu Qing\n\nSichuan agricultural university,China\n\nVersion:V1.0') + + +def main_instructions(): + result_output.insert('1.0', 'Instructions:\n\n1.1. Please click the [Create database] button to set up the database for the first time\n \ + \n2.Input the sequence to be aligned into the text box or select the sequence file through the [Select file] button \ + \n\n3.Select the database to be compared and the comparison method.\n\n4.Set the e-value Value, output format and number of threads.The default e-value =1e-5, and the default output format is 0 and the default of threads is 4\n \ + \n5.Click [Start] button for comparison, and the comparison results will be displayed here and saved in result.txt\n\n6.Alignment time depends on sequence size and computer performance \ + \n') + + +def mkdb_window_cmd(): + make_db() + + +top = Tk() +top.title('BlastGUI') +top.geometry('900x600') + +style = Style() +fnfa = '' +fndb = '' + +db_typeList = get_db_name() +db_type = Combobox(top, text='Select', values=db_typeList, font=('', 13)) +db_type.place(relx=0.129, rely=0.106, relwidth=0.11) + +blast_typeList = ['blastn', 'blastp', 'blastx', 'tblastn', 'tblastx', ] +blast_typeVar = StringVar(value='blastn') +blast_type = Combobox(top, textvariable=blast_typeVar, values=blast_typeList, font=('', 13)) +blast_type.place(relx=0.386, rely=0.1, relwidth=0.08) + +reault_scroll1 = Scrollbar(top, orient='vertical') +reault_scroll1.place(relx=0.959, rely=0.212, relwidth=0.031, relheight=0.758) + +evalueVar = StringVar(value='1e-5') +evalue = Entry(top, textvariable=evalueVar, font=('', 12)) +evalue.place(relx=0.129, rely=0.166, relwidth=0.11, relheight=0.034) + +result_outputFont = Font(font=('', 13)) +result_output = Text(top, yscrollcommand=reault_scroll1.set, font=result_outputFont) +result_output.place(relx=0.02, rely=0.212, relwidth=0.931, relheight=0.773) +main_instructions() +reault_scroll1['command'] = result_output.yview + +star_blastVar = StringVar(value='Start') +style.configure('Tstar_blast.TButton', background='#000000', font=('', 13)) +star_blast = Button(top, text='Start', textvariable=star_blastVar, command=star_blast_cmd, style='Tstar_blast.TButton') +star_blast.place(relx=0.791, rely=0.015, relwidth=0.08, relheight=0.138) + + +style.configure('Tselect_fa_button.TButton', background='#000000', font=('', 13)) +select_fa_button = Button(top, text='Select\n file', command=select_fa_button_Cmd, + style='Tselect_fa_button.TButton') +select_fa_button.place(relx=0.692, rely=0.015, relwidth=0.09, relheight=0.138) + +fa_inputVar = StringVar(value='Enter a sequence here or select a sequence file:') +fa_input = Entry(top, textvariable=fa_inputVar, font=('', 13)) +fa_input.place(relx=0.02, rely=0.015, relwidth=0.654, relheight=0.078) + +aboutVar = StringVar(value='About') +style.configure('Tabout.TButton', font=('', 13)) +about = Button(top, text='About', textvariable=aboutVar, command=about_cmd, style='Tabout.TButton') +about.place(relx=0.88, rely=0.015, relwidth=0.11, relheight=0.065) + +mkdb_windowVar = StringVar(value=' Create\ndatabase') +style.configure('Tmkdb_window.TButton', font=('', 13)) +mkdb_window = Button(top, text='Create database', textvariable=mkdb_windowVar, command=mkdb_window_cmd, style='Tmkdb_window.TButton') +mkdb_window.place(relx=0.88, rely=0.091, relwidth=0.11, relheight=0.065) + +evalue_labelVar = StringVar(value='E-vale：') +style.configure('Tevalue_label.TLabel', anchor='w', font=('', 12)) +evalue_label = Label(top, text='E-vale', textvariable=evalue_labelVar, style='Tevalue_label.TLabel') +evalue_label.place(relx=0.02, rely=0.166, relwidth=0.09, relheight=0.032) + +blast_select_labelVar = StringVar(value='Methods：') +style.configure('Tblast_select_label.TLabel', anchor='w', font=('', 12)) +blast_select_label = Label(top, text='Methods', textvariable=blast_select_labelVar, style='Tblast_select_label.TLabel') +blast_select_label.place(relx=0.267, rely=0.106, relwidth=0.09, relheight=0.032) + +db_selectVar = StringVar(value='Database:') +style.configure('Tdb_select.TLabel', anchor='w', font=('', 12)) +db_select = Label(top, text='Database', textvariable=db_selectVar, style='Tdb_select.TLabel') +db_select.place(relx=0.02, rely=0.106, relwidth=0.09, relheight=0.032) + +outfmt_labelVar = StringVar(value='Outfmt:') +style.configure('Toutfmt_label.TLabel', anchor='w', font=('', 12)) +outfmt_label = Label(top, text='Outfmt', textvariable=outfmt_labelVar, style='Toutfmt_label.TLabel') +outfmt_label.place(relx=0.267, rely=0.166, relwidth=0.09, relheight=0.032) + +outfmt_inputVar = StringVar(value='0') +outfmt_input = Entry(top, textvariable=outfmt_inputVar, font=('', 12)) +outfmt_input.place(relx=0.386, rely=0.166, relwidth=0.08, relheight=0.034) + +threat_labelVar = StringVar(value='Threads:') +style.configure('Tthreat_label.TLabel', anchor='w', font=('', 12)) +threat_label = Label(top, text='Threads:', textvariable=threat_labelVar, style='Tthreat_label.TLabel') +threat_label.place(relx=0.494, rely=0.106, relwidth=0.08, relheight=0.032) + +threat_inputVar = StringVar(value='4') +threat_input = Entry(top, textvariable=threat_inputVar, font=('', 12)) +threat_input.place(relx=0.593, rely=0.106, relwidth=0.08, relheight=0.034) + +top.mainloop()