def run_after(self, rtc, output_dir):
from pbcoretools.pbvalidate import validate_dataset
e, m = validate_dataset(file_name=rtc.task.output_files[0],
dataset_type="ReferenceSet",
validate_index=True,
strict=True)
self.assertEqual(len(e), 0, str(e))
def run_after(self, rtc, output_dir):
from pbcoretools.pbvalidate import validate_dataset
e, m = validate_dataset(
file_name=rtc.task.output_files[0],
dataset_type=self.DATASET_TYPE,
validate_index=True,
strict=True)
self.assertEqual(len(e), 0, str(e))
def run_after(self, rtc, output_dir):
err, metrics = pbvalidate.validate_dataset(
file_name=rtc.task.output_files[0],
dataset_type="SubreadSet",
quick=False,
validate_index=True,
strict=True)
self.assertEqual(len(err), 0)
# TODO replace with BarcodedSubreadSet
with SubreadSet(rtc.task.output_files[0]) as ds:
self.assertEqual(len(ds.externalResources), 1)
self.assertTrue(ds.externalResources[0].scraps is not None)
rr = ds.resourceReaders()[0]
self.assertTrue(rr.pbi.hasBarcodeInfo)
def run_after(self, rtc, output_dir):
err, metrics = pbvalidate.validate_dataset(
file_name=rtc.task.output_files[0],
dataset_type="SubreadSet",
quick=False,
validate_index=True,
strict=True)
self.assertEqual(len(err), 0)
with SubreadSet(rtc.task.output_files[0]) as ds:
self.assertEqual(len(ds.externalResources), 1)
# make sure metadata are propagated
md = ds.metadata
self.assertEqual(
md.collections.submetadata[0].attrib['InstrumentName'],
"Inst54008")
self.assertTrue(ds.externalResources[0].scraps is not None)
self.assertEqual(ds.externalResources[0].barcodes,
self.INPUT_FILES[1])
rr = ds.resourceReaders()[0]
self.assertTrue(rr.pbi.hasBarcodeInfo)
def run_after(self, rtc, output_dir):
err, metrics = pbvalidate.validate_dataset(
file_name=rtc.task.output_files[0],
dataset_type="SubreadSet",
quick=False,
validate_index=True,
strict=True)
self.assertEqual(len(err), 0)
with SubreadSet(rtc.task.output_files[0]) as ds:
self.assertEqual(len(ds.externalResources), 1)
# make sure metadata are propagated
md = ds.metadata
self.assertEqual(
md.collections.submetadata[0].attrib['InstrumentName'],
"Inst54008")
self.assertTrue(ds.externalResources[0].scraps is not None)
self.assertEqual(ds.externalResources[0].barcodes,
self.INPUT_FILES[1])
rr = ds.resourceReaders()[0]
self.assertTrue(rr.pbi.hasBarcodeInfo)
