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])