Source Code for Module Bio.PopGen.SimCoal.Cache

 1  # Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved. 
 2   
 3  """ 
 4  This module allows to cache Simcoal2 results, and return on the fly 
 5  in case the calculation was done. 
 6   
 7  """ 
 8   
 9  import os 
10  import tarfile 
11  from Controller import SimCoalController 
12   
13   
14 -class SimCoalCache(object): 
15 -    def __init__(self, data_dir, simcoal_dir): 
16          """Initializes the cache. 
17   
18          data_dir - Where the cache can be found 
19          simcoal_dir - where the binaries are 
20   
21          IMPORTANT: The cache only makes sense if the file name univocally 
22          identifies the model. 
23            For now use use the model name as key, 
24            and it will probably stay like that. 
25          """ 
26          self.dataDir = data_dir 
27          self.cacheDir = os.sep.join([data_dir, 'SimCoal', 'cache']) 
28          self.simcoalDir = simcoal_dir 
29   
30 -    def run_simcoal(self, par_file, num_sims, ploydi = '1', parDir = None): 
31          if parDir is None: 
32              parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs']) 
33          par_file_root = par_file[:-4] 
34          tar_name = os.sep.join([self.cacheDir, ploydi, par_file_root + 
35              '.tar.bz2']) 
36          if os.access(tar_name, os.R_OK): 
37              tf = tarfile.open(tar_name) 
38              tar_num_sims = len(tf.getmembers()) - 3 
39          else: 
40              tar_num_sims = 0 
41          if tar_num_sims >= num_sims: 
42              tf.extractall(parDir) 
43              tf.close() 
44              return 
45          else: 
46              try: 
47                  tf.close() 
48              except NameError: 
49                  pass  # not opened in the first place, OK. 
50          scc = SimCoalController(self.simcoalDir) 
51          scc.run_simcoal(par_file, num_sims, ploydi, parDir) 
52          tf = tarfile.open(tar_name, 'w:bz2') 
53          tf.add(os.sep.join([parDir, par_file_root]), par_file_root) 
54          tf.close() 
55   
56 -    def listSimulations(self, ploidy = '1'): 
57          ''' 
58             Lists available simulations. 
59          ''' 
60          files = os.listdir(self.cacheDir + os.sep + ploidy) 
61          sims = [] 
62          for file in files: 
63              if file.endswith('.tar.bz2'): 
64                  sims.append(file[:-8]) 
65          return sims 
66   
67 -    def getSimulation(self, sim_name, ploidy = '1', parDir = None): 
68          ''' 
69             Makes available a cached simulation. 
70   
71             @param sim_name simulation name. 
72   
73             This mainly means untaring a file. 
74          ''' 
75          if parDir is None: 
76              parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs']) 
77          tar_name = os.sep.join([self.cacheDir, ploidy, sim_name + 
78              '.tar.bz2']) 
79          tf = tarfile.open(tar_name) 
80          tf.extractall(parDir) 
81          tf.close() 
82   
83   
84  #if __name__ == '__main__': 
85  #  cache = Cache('/home/work/werk/consolidator/sc_cache', 
86  #      '/home/work/software/simcoal') 
87  #  cache.run_simcoal('.', 'island_snp-50_0.0025_10_0.083_100_60.par', 102) 
88