def illustrate(args):
data = json.load(file(args.file))
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
testsuites = {}
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
analyser = analyse.Analyser()
lo.info('loading json-file args.file')
analyser.decode(testsuites, data)
lo.info('updating testsuites')
analyser.update_testsuites()
if args.readlengths:
rls = analyser.stats['readlengths']
hist = TextHist()
print(hist.draw(rls, indexed=True))
if args.coverage:
for name, testsuite in analyser.testsuites.items():
print(name + ':')
for test in testsuite.tests:
print(' - %s : %s' % (test, analyser[test]))
print()
if args.results:
for testsuite, results in analyser.results.items():
print('\n'+testsuite)
print('-'*len(testsuite))
pprint(results)
def __init__(self, jpath_or_analyser, testsuites, testsuite_paths):
self.win = ThemedTk(title='json explorer', esc_closes=True,
geometry=(-200, -200))
if sys.platform == 'win32':
self.win.wm_iconbitmap(bitmap = get_root_path('res', 'TPH_DNA.ico'))
self.win.columnconfigure(0, weight=1)
self.win.columnconfigure(1, weight=0)
self.win.rowconfigure(0, weight=0)
self.win.rowconfigure(1, weight=0)
self.win.rowconfigure(2, weight=4)
if isinstance(jpath_or_analyser, Analyser):
self.analyser = jpath_or_analyser
name = os.path.basename(self.analyser.fastq.fname)
else:
try:
data = json.load(file(jpath_or_analyser))
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
self.analyser = Analyser()
self.analyser.decode(testsuites, data)
self.analyser.update_testsuites()
except Exception, e:
exc_info = sys.exc_info()
self.win.destroy()
raise exc_info[1], None, exc_info[2]
name = os.path.basename(jpath_or_analyser)
def test_update_testsuites(self):
v = StrictVersion(self.testsuites['MTBC/test'].version)
# load by full name
testsuites = {}
update_testsuites(testsuites,
{'MTBC/test': str(v)},
self.testsuite_paths
)
assert testsuites.keys() == ['MTBC/test']
# load by short name
update_testsuites(testsuites,
{'test': str(v)},
self.testsuite_paths
)
assert set(testsuites.keys()) == set(['MTBC/test', 'test'])
assert testsuites['test'] == testsuites['MTBC/test']
# load compatible
vv = list(v.version)
vv[1] -= 1
v.version = vv
update_testsuites(testsuites,
{'test': str(v)},
self.testsuite_paths
)
assert set(testsuites.keys()) == set(['MTBC/test', 'test'])
# load incompatbile 1/2
vv[1] += 2
v.version = vv
try:
update_testsuites(testsuites,
{'test': str(v)},
self.testsuite_paths
)
assert False, 'future minor version specified; should fail'
except TestsuiteVersionConflictException:
pass
# load incompatbile 1/2
vv[1] -= 1
vv[0] -= 1
v.version = vv
try:
update_testsuites(testsuites,
{'test': str(v)},
self.testsuite_paths
)
assert False, 'different major version specified; should fail'
except TestsuiteVersionConflictException:
pass
def update(args):
if args.fastq:
lo.warning('re-reading of hits not currently implemented')
data = json.load(file(args.json))
testsuite_paths = discover_testsuites(args.testsuite_directory or [])
testsuites = {}
update_testsuites(testsuites, data['info']['testsuites'], testsuite_paths)
analyser = analyse.Analyser()
analyser.decode(testsuites, data)
analyser.update_testsuites()
# save results back to .json
data = analyser.encode(hits = analyser.hits is not None)
j = codecs.open(args.json, 'w', 'utf-8')
lo.info('re-wrote results to file ' + args.json)
json.dump(data, j, indent=2)
