Package Bio :: Package PopGen :: Package SimCoal :: Module Cache
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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  from logging import debug 
10  from sys import exit 
11  import os 
12  import tarfile 
13  import tempfile 
14  from Controller import SimCoalController 
15   
16 -class SimCoalCache(object):
17 - def __init__(self, data_dir, simcoal_dir):
18 """Initializes the cache. 19 20 data_dir - Where the cache can be found 21 simcoal_dir - where the binaries are 22 23 IMPORTANT: The cache only makes sense if the file name univocally 24 identifies the model. 25 For now use use the model name as key, 26 and it will probably stay like that. 27 """ 28 self.dataDir = data_dir 29 self.cacheDir = os.sep.join([data_dir, 'SimCoal', 'cache']) 30 self.simcoalDir = simcoal_dir
31 32
33 - def run_simcoal(self, par_file, num_sims, ploydi = '1', parDir = None):
34 if parDir == None: 35 parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs']) 36 par_file_root = par_file[:-4] 37 tar_name = os.sep.join([self.cacheDir, ploydi, par_file_root + 38 '.tar.bz2']) 39 if os.access(tar_name, os.R_OK): 40 tf = tarfile.open(tar_name) 41 tar_num_sims = len(tf.getmembers()) - 3 42 else: 43 tar_num_sims = 0 44 if tar_num_sims >= num_sims: 45 tf.extractall(parDir) 46 tf.close() 47 return 48 else: 49 try: 50 tf.close() 51 except NameError: 52 pass #not opened in the first place, OK. 53 scc = SimCoalController(self.simcoalDir) 54 scc.run_simcoal(par_file, num_sims, ploydi, parDir) 55 tf = tarfile.open(tar_name, 'w:bz2') 56 tf.add(os.sep.join([parDir, par_file_root]), par_file_root) 57 tf.close()
58
59 - def listSimulations(self, ploidy = '1'):
60 ''' 61 Lists available simulations. 62 ''' 63 files = os.listdir(self.cacheDir + os.sep + ploidy) 64 sims = [] 65 for file in files: 66 if file.endswith('.tar.bz2'): 67 sims.append(file[:-8]) 68 return sims
69
70 - def getSimulation(self, sim_name, ploidy = '1', parDir = None):
71 ''' 72 Makes available a cached simulation. 73 74 @param sim_name simulation name. 75 76 This mainly means untaring a file. 77 ''' 78 if parDir == None: 79 parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs']) 80 tar_name = os.sep.join([self.cacheDir, ploidy, sim_name + 81 '.tar.bz2']) 82 tf = tarfile.open(tar_name) 83 tf.extractall(parDir) 84 tf.close()
85 86 87 #if __name__ == '__main__': 88 # cache = Cache('/home/work/werk/consolidator/sc_cache', 89 # '/home/work/software/simcoal') 90 # cache.run_simcoal('.', 'island_snp-50_0.0025_10_0.083_100_60.par', 102) 91