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Viewing changes to Bio/PopGen/SimCoal/Cache.py

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2014-06-08 10:25:35 UTC
  • mfrom: (1.1.22)
  • Revision ID: package-import@ubuntu.com-20140608102535-ebgnhcpcrum3i3w8
Tags: 1.64+dfsg-1
http://bugs.debian.org/750845
* New upstream version
* Build-Depends raxml only on those architectures where it is available
  Closes: #750845

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Bio/PopGen/SimCoal/Cache.py
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# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>.  All rights reserved.
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"""
 
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(DEPRECATED)
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This module allows to cache Simcoal2 results, and return on the fly
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in case the calculation was done.
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        self.cacheDir = os.sep.join([data_dir, 'SimCoal', 'cache'])
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        self.simcoalDir = simcoal_dir
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    def run_simcoal(self, par_file, num_sims, ploydi = '1', parDir = None):
 
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    def run_simcoal(self, par_file, num_sims, ploydi='1', parDir=None):
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        if parDir is None:
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            parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs'])
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        par_file_root = par_file[:-4]
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        tar_name = os.sep.join([self.cacheDir, ploydi, par_file_root +
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            '.tar.bz2'])
 
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                                '.tar.bz2'])
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        if os.access(tar_name, os.R_OK):
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            tf = tarfile.open(tar_name)
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            tar_num_sims = len(tf.getmembers()) - 3
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        tf.add(os.sep.join([parDir, par_file_root]), par_file_root)
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        tf.close()
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    def listSimulations(self, ploidy = '1'):
 
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    def listSimulations(self, ploidy='1'):
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        '''
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           Lists available simulations.
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        '''
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                sims.append(file[:-8])
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        return sims
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    def getSimulation(self, sim_name, ploidy = '1', parDir = None):
 
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    def getSimulation(self, sim_name, ploidy='1', parDir=None):
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        '''
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           Makes available a cached simulation.
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        if parDir is None:
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            parDir = os.sep.join([self.dataDir, 'SimCoal', 'runs'])
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        tar_name = os.sep.join([self.cacheDir, ploidy, sim_name +
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            '.tar.bz2'])
 
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                                '.tar.bz2'])
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        tf = tarfile.open(tar_name)
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        tf.extractall(parDir)
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        tf.close()