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):
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'))