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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: Sat Dec 2 16:02:17 2000
# thomas@cbs.dtu.dk, http://www.cbs.dtu.dk/thomas
# File: xbb_blastbg.py
from __future__ import print_function
import os
import tempfile
import threading
try:
import tkMessageBox as messagebox # Python 2
except ImportError:
from tkinter import messagebox # Python 3
from Bio.Blast.Applications import (NcbiblastnCommandline,
NcbiblastpCommandline,
NcbiblastxCommandline,
NcbitblastnCommandline,
NcbitblastxCommandline)
class BlastDisplayer(object):
def __init__(self, command_data, text_id=None):
self.command_data = command_data
self.tid = text_id
def RunCommand(self):
self.fh_in, self.infile = tempfile.mkstemp()
self.fh_out, self.outfile = tempfile.mkstemp()
with open(self.infile, 'w+') as f:
f.write('>Name\n')
f.write(self.command_data[0])
blast_program = self.command_data[1]
database = self.command_data[2]
# Check if user supplied additional options and extract them
if self.command_data[3]:
option = self.command_data[3]
options = {}
for x in range(0, len(option.split()) - 1, 2):
options[option.split()[x]] = option.split()[x + 1]
else:
options = {}
args, kwargs = blast_program, {'query': self.infile, 'db': database,
'out': self.outfile}
if blast_program.endswith('blastn'):
blast_cmd = NcbiblastnCommandline(args, **kwargs)
elif blast_program.endswith('blastp'):
blast_cmd = NcbiblastpCommandline(args, **kwargs)
elif blast_program.endswith('blastx'):
blast_cmd = NcbiblastxCommandline(args, **kwargs)
elif blast_program.endswith('tblastn'):
blast_cmd = NcbitblastnCommandline(args, **kwargs)
elif blast_program.endswith('tblastx'):
blast_cmd = NcbitblastxCommandline(args, **kwargs)
else:
return
if options:
try:
for key in options:
blast_cmd.set_parameter(key, options[key])
except ValueError as e:
messagebox.showerror('xbb tools',
'Commandline error:\n\n' + str(e))
self.tid.destroy()
return
self.worker = BlastWorker(blast_cmd)
self.worker.start()
self.UpdateResults()
def UpdateResults(self):
# open the oufile and displays new appended text
self.tid.insert('end', 'BLAST is running...')
while True:
self.tid.update()
if self.worker.finished:
self.tid.delete('1.0', 'end')
break
with open(self.outfile) as fid:
try:
txt = fid.read()
self.tid.insert('end', txt)
self.tid.update()
except:
# text widget is detroyed, we assume the search
# has been cancelled
pass
self.Exit()
def Exit(self):
if os.path.exists(self.outfile):
os.close(self.fh_out)
os.remove(self.outfile)
if os.path.exists(self.infile):
os.close(self.fh_in)
os.remove(self.infile)
del self.worker
class BlastWorker(threading.Thread):
def __init__(self, blast_command):
self.com = blast_command
threading.Thread.__init__(self)
self.finished = 0
def run(self):
try:
self.com()
except Exception as e:
messagebox.showwarning('BLAST error',
'BLAST error:\n\n' + str(e))
self.finished = 1
if __name__ == '__main__':
os.system('python xbb_blast.py' +
' ATGACAAAGCTAATTATTCACTTGGTTTCAGACTCTTCTGTGCAAACTGC')
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