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'))
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)
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'))