def test_ccsset_from_bam(self):
# DONE bug 28698
ds1 = ConsensusReadSet(upstreamData.getCCSBAM(), strict=False)
fn = tempfile.NamedTemporaryFile(suffix=".consensusreadset.xml").name
log.debug(fn)
ds1.write(fn, validate=False)
ds1.write(fn)
def test_ccsset_from_bam(self):
# DONE bug 28698
ds1 = ConsensusReadSet(upstreamData.getCCSBAM(), strict=False)
fn = tempfile.NamedTemporaryFile(suffix=".consensusreadset.xml").name
log.debug(fn)
ds1.write(fn, validate=False)
ds1.write(fn)
def run_args(args):
dstore = DataStore.load_from_json(os.path.realpath(args.datastore))
ds_in = ConsensusReadSet(args.ccs_in, trustCounts=True)
ds_out = ConsensusReadSet(*([f.path for f in dstore.files.values()]),
trustCounts=True)
sanitize_dataset_tags(ds_out, remove_hidden=True)
ds_out.name = ds_in.name.replace(" (filtered)", "") + " (trimmed)"
ds_out.subdatasets = []
ds_out.write("trimmed.consensusreadset.xml")
return 0
def _run_args(args):
ds = ConsensusReadSet(args.ccsxml, strict=True)
orig_uuid = ds.uuid
ds.consolidate("reads.bam", useTmp=False)
bam_res = ds.externalResources[0]
if args.zmws_json:
bam_res._setSubResByMetaType("PacBio.FileTypes.json", args.zmws_json)
if args.report_ccs_processing:
bam_res._setSubResByMetaType("PacBio.FileTypes.JsonReport",
args.report_ccs_processing)
ds.uuid = orig_uuid
ds.write("final.consensusreadset.xml")
with open("reads.fofn", "wt") as fofn:
fofn.write(os.path.abspath("reads.bam"))
return 0
def setUpData(cls):
cls.bam_file_name = pbcore.data.getCCSBAM()
cls.xml_file_name = tempfile.NamedTemporaryFile(
suffix=".consensusreadset.xml").name
ds = ConsensusReadSet(cls.bam_file_name)
ds.write(cls.xml_file_name)
def setUpClass(cls):
super(TestToolContract, cls).setUpClass()
ds = ConsensusReadSet(pbcore.data.getCCSBAM(), strict=True)
ds.write(cls.INPUT_FILES[0])
def setUpClass(cls):
ds = ConsensusReadSet(pbcore.data.getCCSBAM(), strict=True)
ds.write(cls.INPUT_FILES[0])
def setUpClass(cls):
ds = ConsensusReadSet(pbcore.data.getCCSBAM(), strict=True)
ds.write(cls.INPUT_FILES[0])
