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| #!/usr/bin/env python | ||
| # -*- coding:utf-8 -*- | ||
| # Author：Wu Qing | ||
| # E-mail: cipn@qq.com | ||
|
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| 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 | ||
|
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|
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| 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!") | ||
|
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||
| def select_fadb_button_cmd(): | ||
| global fndb | ||
| fndb = tkinter.filedialog.askopenfilename() | ||
| make_db_label.config(text="The files you selected:\n" + fndb) | ||
|
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||
| 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") | ||
|
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| dbwindow = Tk() | ||
| dbwindow.title('Create database') | ||
| dbwindow.geometry('600x400') | ||
|
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| 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) | ||
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| 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() | ||
|
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
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| 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) | ||
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| dbwindow.mainloop() | ||
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| 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 | ||
|
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| # 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 | ||
|
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|
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| # blast process | ||
| def star(): | ||
| fnfa_stat = "The files you selected:" + fnfa | ||
| fain_stat = fa_input.get() | ||
|
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| if fnfa_stat == fain_stat: | ||
| fa = fnfa | ||
| else: | ||
| fa = 'tmp.txt' | ||
|
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| 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() | ||
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||
| 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!') | ||
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| 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 | ||
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| 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 | ||
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| def about_cmd(): | ||
| showinfo(title='Abount', message='BlstaGUI\n\nAuthor：Wu Qing\n\nSichuan agricultural university,China\n\nVersion:V1.0') | ||
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| 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') | ||
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| def mkdb_window_cmd(): | ||
| make_db() | ||
|
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| top = Tk() | ||
| top.title('BlastGUI') | ||
| top.geometry('900x600') | ||
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| style = Style() | ||
| fnfa = '' | ||
| fndb = '' | ||
|
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| 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) | ||
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| 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) | ||
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| reault_scroll1 = Scrollbar(top, orient='vertical') | ||
| reault_scroll1.place(relx=0.959, rely=0.212, relwidth=0.031, relheight=0.758) | ||
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| 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) | ||
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| 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 | ||
|
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| 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) | ||
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| 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) | ||
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| 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) | ||
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| 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) | ||
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
|
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| 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) | ||
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| 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) | ||
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| top.mainloop() |