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#!/usr/bin/env python
# Copyright 2000 by Thomas Sicheritz-Ponten.
# Copyright 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
"""BLAST code for graphical Xbbtools tool."""
import os
import tempfile
import threading
from tkinter import messagebox
from tkinter import Tk
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast.Applications import NcbiblastpCommandline
from Bio.Blast.Applications import NcbiblastxCommandline
from Bio.Blast.Applications import NcbitblastnCommandline
from Bio.Blast.Applications import NcbitblastxCommandline
class BlastDisplayer:
"""A class for running and displaying a BLAST search."""
def __init__(self, command_data, text_id=None):
"""Take command data and notpad id."""
self.command_data = command_data
self.tid = text_id
def RunCommand(self):
"""Run the BLAST search."""
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):
"""Write BLAST result data into notepad."""
# 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 Exception:
# text widget is destroyed, we assume the search
# has been cancelled
pass
self.Exit()
def Exit(self):
"""Clean up on exit."""
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):
"""Allows multiple BLAST searches by threading."""
def __init__(self, blast_command):
"""Initialize the worker."""
self.com = blast_command
threading.Thread.__init__(self)
self.finished = 0
def run(self):
"""Start worker."""
try:
self.com()
except Exception as e:
messagebox.showwarning("BLAST error", "BLAST error:\n\n" + str(e))
self.finished = 1
if __name__ == "__main__":
from xbb_blast import BlastIt
win = Tk()
win.title("Dummy windows for BLAST test")
test = BlastIt("ATGACAAAGCTAATTATTCACTTGGTTTCAGACTCTTCTGTGCAAACTGC")
win.mainloop()
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