Source Code for Module Bio.PopGen.SimCoal.Controller

 1  # Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5   
 6  """ 
 7  This module allows you to control Simcoal2. 
 8   
 9  """ 
10   
11  import os 
12  import sys 
13   
14   
15 -class SimCoalController(object): 
16 -    def __init__(self, simcoal_dir): 
17          """Initializes the controller. 
18   
19          simcoal_dir is the directory where simcoal is. 
20   
21          The initializer checks for existance and executability of binaries. 
22          """ 
23          self.simcoal_dir = simcoal_dir 
24          self.os_name = os.name  # remove this? 
25          dir_contents = os.listdir(self.simcoal_dir) 
26          #We expect the tool to be installed as simcoal2(.exe) 
27          #without any trailing version number. 
28          self.bin_name = "simcoal2" 
29          if self.bin_name not in dir_contents: 
30              #Try case insensitive, 
31              dir_contents = [x.lower() for x in dir_contents] 
32          if self.bin_name not in dir_contents: 
33              #Try with .exe 
34              self.bin_name += '.exe' 
35          if self.bin_name not in dir_contents: 
36              raise IOError("SimCoal not available") 
37          if not os.access(os.path.join(self.simcoal_dir, self.bin_name), 
38                           os.X_OK): 
39              raise IOError("SimCoal not executable") 
40   
41 -    def run_simcoal(self, par_file, num_sims, ploydi = '1', par_dir = '.'): 
42          """Executes SimCoal. 
43          """ 
44          if par_dir is None: 
45              par_dir = os.sep.join([".", 'SimCoal', 'runs']) 
46          curr_dir = os.getcwd() 
47          #TODO - Make sure we change drive on Windows as well? 
48          os.chdir(par_dir) 
49          exe = os.path.join(self.simcoal_dir, self.bin_name) 
50          if " " in exe: 
51              exe = '"' + exe + '"' 
52          cmd = exe + ' ' + par_file + ' ' + str(num_sims) + ' ' + ploydi 
53          #TODO - Better way to spot if on Jython on Windows? 
54          if sys.platform=="win32" or self.bin_name.endswith(".exe"): 
55              #There is no /dev/nul on Windows 
56              cmd += ' > nul 2>nul' 
57          else: 
58              cmd += ' >/dev/null 2>&1' 
59          os.system(cmd) 
60          os.chdir(curr_dir) 
61