Python runCommands示例

示例#1

文件： comparatorWrapper.py 项目： dentearl/mwgAlignAnalysis

def callEvaluation(options):
   cmds = []
   for t in ['MRCA', 'MRCAnp', 'ROOT', 'ROOTnp']:
      filename = 'comparator%s.xml' % t
      if os.path.exists(os.path.join(options.outDir, filename)):
         # these four analyses can take a long time to run, crashes should not force an entire restart,
         # just a partial restart. This conditional allows analysis checkpointing.
         continue
      cmd = libComparator.basicCommand(filename + '.tmp', 'truth%s' % t, options)
      cmds.append(cmd)
      cmds.append(libComparator.moveCommand(os.path.join(options.outDir, filename + '.tmp'), 
                                            os.path.join(options.outDir, filename)))
   libWrapper.runCommands(cmds, os.curdir)
   libWrapper.recordCommands(cmds, os.path.join(options.outDir, 'commands.txt'))

示例#2

文件： coverageCopyNumWrapper.py 项目： dentearl/mwgAlignAnalysis

def callEvaluation(options):
   pickle = os.path.join(options.outDir, 'mafCoverageCopyNum.pickle')

   # create mafCoveragePickle
   cmd = ['mafCoveragePickleCreator.py']
   cmd.append('--maf=%s' % options.predMaf)
   cmd.append('--species=%s' % ','.join(options.reg['species']))
   cmd.append('--pickle=%s' % pickle)
   libWrapper.runCommands([cmd], os.curdir)
   
   # perform gap analysis:
   cmd = ['mafCoveragePickleAnalysis.py']
   cmd.append('--pickle=%s' % pickle)
   cmd.append('--outfile=%s' % os.path.join(options.outDir, 'coverageCopyNumSummary.xml'))
   libWrapper.runCommands([cmd], os.curdir)

示例#3

文件： coverageCopyNumWrapper.py 项目： wangdi2014/mwgAlignAnalysis

def callEvaluation(options):
    pickle = os.path.join(options.outDir, 'mafCoverageCopyNum.pickle')

    # create mafCoveragePickle
    cmd = ['mafCoveragePickleCreator.py']
    cmd.append('--maf=%s' % options.predMaf)
    cmd.append('--species=%s' % ','.join(options.reg['species']))
    cmd.append('--pickle=%s' % pickle)
    libWrapper.runCommands([cmd], os.curdir)

    # perform gap analysis:
    cmd = ['mafCoveragePickleAnalysis.py']
    cmd.append('--pickle=%s' % pickle)
    cmd.append('--outfile=%s' %
               os.path.join(options.outDir, 'coverageCopyNumSummary.xml'))
    libWrapper.runCommands([cmd], os.curdir)

示例#4

文件： comparatorRepeatsWrapper.py 项目： wangdi2014/mwgAlignAnalysis

def callEvaluation(options):
   annots = libComparator.getAnnots('repeats', options)
   cmds = []
   for t in ['MRCA', 'MRCAnp', 'ROOT', 'ROOTnp']:
      filename = 'comparator%sRepeats.xml' % t
      if os.path.exists(os.path.join(options.outDir, filename)):
         # these four analyses can take a long time to run, crashes should not force an entire restart,
         # just a partial restart. This conditional allows analysis checkpointing.
         continue
      cmd = libComparator.basicCommand(filename + '.tmp', 'truth%s' % t, options)
      cmd.append('--bedFiles=%s' % ','.join(annots))
      cmds.append(cmd)
      cmds.append(libComparator.moveCommand(os.path.join(options.outDir, filename + '.tmp'), 
                                            os.path.join(options.outDir, filename)))
   libWrapper.runCommands(cmds, os.curdir)
   libWrapper.recordCommands(cmds, os.path.join(options.outDir, 'commands.txt'))