def test_find_samples(self):
plist = find_samples(j_doe_00_01)
self.assertEqual([os.path.basename(x) for x in plist], ALLSAMPLES)
plist = find_samples(j_doe_00_01, sample="P111")
self.assertEqual([os.path.basename(x) for x in plist], [])
plist = find_samples(j_doe_00_01, sample=SAMPLE)
self.assertEqual([os.path.basename(x) for x in plist], [SAMPLE])
plist = find_samples(j_doe_00_01, sample="P001")
self.assertEqual([os.path.basename(x) for x in plist], [])
samplefile = os.path.join(j_doe_00_01, "samples.txt")
with open(samplefile, "w") as fh:
fh.write(SAMPLE)
plist = find_samples(j_doe_00_01, sample=samplefile)
self.assertEqual([os.path.basename(x) for x in plist], [SAMPLE])
def test_find_samples(self):
plist = find_samples(j_doe_00_01)
self.assertEqual([os.path.basename(x) for x in plist], ALLSAMPLES)
plist = find_samples(j_doe_00_01, sample="P111")
self.assertEqual([os.path.basename(x) for x in plist], [])
plist = find_samples(j_doe_00_01, sample=SAMPLE)
self.assertEqual([os.path.basename(x) for x in plist], [SAMPLE])
plist = find_samples(j_doe_00_01, sample="P001")
self.assertEqual([os.path.basename(x) for x in plist], [])
samplefile = os.path.join(j_doe_00_01, "samples.txt")
with open(samplefile, "w") as fh:
fh.write(SAMPLE)
plist = find_samples(j_doe_00_01, sample=samplefile)
self.assertEqual([os.path.basename(x) for x in plist], [SAMPLE])
def run_halo(path=None, project=None, batch_size=8, **kw):
"""Run halo application. Setup parameter files and call
halo_pipeline.sh script.
:param project: project name
:param batch_size: number of samples to run in each project config file
"""
plist = sorted(find_samples(path, **kw))
plist_chunks=[plist[x:x+batch_size] for x in xrange(0, len(plist), batch_size)]
i = 0
param_list = []
for pl in plist_chunks:
i += 1
outfile = os.path.join(path, "{}_{}_halo.projectrc".format(project, i))
param = {'cl':None, 'platform_args':None, 'workingDirectory':None}
label = '{}_halo_{}'.format(project[0:3].replace(".", "_"), i)
d = {'samples' : '"{}"'.format(" ".join([os.path.basename(x) for x in pl])),
'indir' : path,
'baits_file' : kw.get('baits', ""),
'targets_file' : kw.get('targets', ""),
'target_region' : kw.get('target_region', ""),
'output' : os.path.join(os.path.dirname(outfile), "{}.out".format(label)),
'error' : os.path.join(os.path.dirname(outfile), "{}.err".format(label))
}
if kw.get("setup", False):
dry_write(outfile, PROJECTTEMPLATE.render(**d), dry_run=kw.get("dry_run", False))
if not os.path.exists(outfile):
LOG.warn("No such configuration file {}; rerun command with '--setup' option")
return []
if kw.get("config", None) and os.path.basename(outfile) != kw.get("config", None):
continue
param['cl'] = [HALOSCRIPT, "-c", HALORC, outfile]
param['platform_args'] = ['--output', os.path.join("{}.out".format(label)),
'--error', os.path.join("{}.err".format(label)),
'--job-name', label]
param['workingDirectory'] = os.path.dirname(outfile)
param_list.append(param)
return param_list