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#!/usr/bin/env python
# Copyright 2000 by Thomas Sicheritz-Ponten.
# Copyrigth 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.
# Created: Thu Jul 13 14:07:25 2000
# thomas@cbs.dtu.dk, http://www.cbs.dtu.dk/thomas
# File: xbb_blast.py
from __future__ import print_function
import glob
import os
import sys
try: # Python 2
import Tkinter as tk
import ttk
import tkFileDialog as filedialog
import tkMessageBox as messagebox
except ImportError: # Python 3
import tkinter as tk
import tkinter.ttk as ttk
from tkinter import filedialog
from tkinter import messagebox
from xbb_utils import NotePad
import xbb_blastbg
class BlastIt(object):
nin, pin = [], []
blast_ok = False
blast_path = ''
def __init__(self, seq, parent=None):
self.seq = seq
self.parent = parent
self.toplevel = tk.Toplevel(parent)
self.toplevel.title('BLAST parameters')
if not self.get_blast_databases() or not self.get_blast_binaries():
return
self.Choices()
self.dbs.bind('<<ComboboxSelected>>', self.Validate)
self.blasts.bind('<<ComboboxSelected>>', self.Validate)
def get_blast_databases(self):
"""Try to locate the BLAST databases and put into lists."""
if not (BlastIt.nin and BlastIt.pin):
pin, nin = [], []
try:
pin.extend(glob.glob(os.environ['BLASTDB'] + '/*.pin'))
except KeyError:
pass
pin.extend(glob.glob('C:*.pin'))
try:
nin.extend(glob.glob(os.environ['BLASTDB'] + '/*.nin'))
except KeyError:
pass
# If no system variable BLASTDB exists, give user the chance to
# locate his database folder:
if not(nin and pin):
database_folder = filedialog.askdirectory(
title='Please locate your BLAST database(s) folder:')
nin.extend(glob.glob(database_folder + '/*.nin'))
pin.extend(glob.glob(database_folder + '/*.pin'))
if not (nin and pin):
messagebox.showerror('xbb tools', 'This folder does not'
' contain any BLAST databases!')
self.toplevel.destroy()
return False
self.pin = [os.path.splitext(x)[0] for x in pin]
self.nin = [os.path.splitext(x)[0] for x in nin]
BlastIt.pin = self.pin
BlastIt.nin = self.nin
return True
def get_blast_binaries(self):
"""Test if BLAST binaries are in PATH or let user locate them."""
if not BlastIt.blast_ok:
# Test if blast binaries are in path
if os.system('blastn -version'): # Return of non-zero means error
self.blast_path = filedialog.askdirectory(
title='Please locate your BLAST program folder:')
self.blast_path += os.sep
if os.system('{}blastn -version'.format(self.blast_path)):
messagebox.showerror(
'xbb tools', 'Wrong folder or missing BLAST'
' binaries!\n To run BLAST you must install the '
' standalone BLAST binaries.')
self.toplevel.destroy()
return False
else:
BlastIt.blast_ok = True
else: # BLAST binaries are in PATH
BlastIt.blast_ok = True
self.blast_path = ''
BlastIt.blast_path = self.blast_path
self.toplevel.lift()
return True
def database_readable(self, db_paths):
"""Return the name of the blast database without path and extension."""
db_names = [entry.split(os.sep)[-1].split('.')[0]
for entry in db_paths]
return db_names
def convert_dbname_to_dbpath(self, db_name):
"""Return the full path for a given blast database name."""
database_path = ''
for database in self.nin:
if database.endswith(db_name):
database_path = database
break
for database in self.pin:
if database.endswith(db_name):
database_path = database
break
return database_path
def Choices(self):
self.blast_string = tk.StringVar()
self.blast_string.set('blastn')
self.cf = ttk.Frame(self.toplevel)
self.cf.pack(side='top', expand=1, fill='x')
self.dbs_frame = ttk.LabelFrame(self.cf, text='Databases')
self.dbs_frame.pack(side='left', padx=5, pady=5, expand=1, fill='x')
nin_values = self.database_readable(self.nin)
pin_values = self.database_readable(self.pin)
self.dbs = ttk.Combobox(self.dbs_frame, exportselection=0,
values=nin_values + pin_values)
self.dbs.current(0)
self.blast_frame = ttk.LabelFrame(self.cf, text='BLAST programs')
self.blast_frame.pack(side='left', padx=5, pady=5, expand=1, fill='x')
self.blasts = ttk.Combobox(self.blast_frame, exportselection=0,
textvariable=self.blast_string,
values=['blastn', 'blastp', 'blastx',
'tblastn', 'tblastx'])
self.dbs.pack(side='left', padx=5, pady=5, expand=1, fill='x')
self.blasts.pack(side='left', padx=5, pady=5, expand=1, fill='x')
self.option_f = ttk.LabelFrame(self.cf, text='Command line options')
self.option_f.pack(side='left', padx=5, pady=5, expand=1, fill='x')
self.option = ttk.Entry(self.option_f)
self.option.pack(side='left', padx=5, pady=5, fill='x', expand=1)
self.ok = ttk.Button(self.cf, text='Run', command=self._Run,
state='disabled')
self.ok.pack(side='right')
self.Validate()
def Validate(self, *args):
db = self.convert_dbname_to_dbpath(self.dbs.get())
prog = self.blasts.get()
if (prog in ['blastn', 'tblastx', 'tblastn']) == (db in self.nin):
self.ok.config(state='normal')
elif (prog in ['blastp', 'blastx']) == (db in self.pin):
self.ok.config(state='normal')
else:
self.ok.config(state='disabled')
def _Run(self):
"""Setup options for Blast commandline (PRIVATE)."""
command_options = self.option.get()
options = ''
if len(command_options.strip()):
options = command_options.strip()
db = self.convert_dbname_to_dbpath(self.dbs.get())
prog = self.blast_path + self.blasts.get()
self.command_data = [self.seq, prog, db, options]
self.Run()
def Run(self):
self.notepad = NotePad()
tid = self.notepad.tid
self.toplevel.destroy()
blastbg = xbb_blastbg.BlastDisplayer(self.command_data, tid)
blastbg.RunCommand()
if __name__ == '__main__':
try:
seq = sys.argv[1]
except IndexError: # Started script without providing a sequence
seq = 'ATGACAAAGCTAATTATTCACTTGGTTTCAGACTCTTCTGTGCAAACTGC'
win = tk.Tk()
win.title('Dummy windows for BLAST test')
test = BlastIt(seq)
win.mainloop()
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