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# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. All rights reserved.
"""Cache for Simcoal2 results (DEPRECATED).
This module allows you to cache Simcoal2 results, and return on the fly
in case the calculation was done.
"""
import os
import tarfile
from .Controller import SimCoalController
class SimCoalCache(object):
def __init__(self, data_dir, simcoal_dir):
"""Initializes the cache.
- data_dir - Where the cache can be found
- simcoal_dir - where the binaries are
IMPORTANT: The cache only makes sense if the file name univocally
identifies the model.
For now use use the model name as key,
and it will probably stay like that.
"""
self.dataDir = data_dir
self.cacheDir = os.sep.join([data_dir, 'SimCoal', 'cache'])
self.simcoalDir = simcoal_dir
def run_simcoal(self, par_file, num_sims, ploydi='1', parDir=None):
if parDir is None:
parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs'])
par_file_root = par_file[:-4]
tar_name = os.sep.join([self.cacheDir, ploydi, par_file_root +
'.tar.bz2'])
if os.access(tar_name, os.R_OK):
tf = tarfile.open(tar_name)
tar_num_sims = len(tf.getmembers()) - 3
else:
tar_num_sims = 0
if tar_num_sims >= num_sims:
tf.extractall(parDir)
tf.close()
return
else:
try:
tf.close()
except NameError:
pass # not opened in the first place, OK.
scc = SimCoalController(self.simcoalDir)
scc.run_simcoal(par_file, num_sims, ploydi, parDir)
tf = tarfile.open(tar_name, 'w:bz2')
tf.add(os.sep.join([parDir, par_file_root]), par_file_root)
tf.close()
def listSimulations(self, ploidy='1'):
"""
Lists available simulations.
"""
files = os.listdir(self.cacheDir + os.sep + ploidy)
sims = []
for file in files:
if file.endswith('.tar.bz2'):
sims.append(file[:-8])
return sims
def getSimulation(self, sim_name, ploidy='1', parDir=None):
"""Makes available a cached simulation.
@param sim_name simulation name.
This mainly means untaring a file.
"""
if parDir is None:
parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs'])
tar_name = os.sep.join([self.cacheDir, ploidy, sim_name +
'.tar.bz2'])
tf = tarfile.open(tar_name)
tf.extractall(parDir)
tf.close()
# if __name__ == '__main__':
# cache = Cache('/home/work/werk/consolidator/sc_cache',
# '/home/work/software/simcoal')
# cache.run_simcoal('.', 'island_snp-50_0.0025_10_0.083_100_60.par', 102)
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