def _create_barcode_report(self): """ Creates and returns a Barcode Report """ from pbreports.report.barcode import run_to_report, _to_tuple_list from test_pbreports_report_barcode import _DATA_DIR as datadir log.info('Creating Barcode report using datadir {d}'.format(d=datadir)) bas_h5_fofn = os.path.join(datadir, 'bash5.fofn') barcode_h5_fofn = os.path.join(datadir, 'barcodeh5.fofn') bas_barcode_list = _to_tuple_list(bas_h5_fofn, barcode_h5_fofn) report_json = 'barcode.json' output_json = os.path.join(self._output_dir, report_json) use_subreads = True report = run_to_report(bas_barcode_list, subreads=use_subreads) pformat(report.to_dict()) report.write_json(output_json) return self._deserialize_report(output_json)
def _create_long_amplicon_report(self): """ Creates a Long Amplicon Report """ from pbreports.report.long_amplicon_analysis import run_to_report from test_pbreports_report_long_amplicon_analysis import DATA_DIR as datadir log.info('Creating Long Amplicon report using datadir {d}'.format( d=datadir)) input_name = 'amplicon_assembly.csv' file_name = os.path.join(datadir, input_name) report_json = 'long_amplicon.json' output_json = os.path.join(self._output_dir, report_json) report = run_to_report(file_name) pformat(report.to_dict()) report.write_json(output_json) return self._deserialize_report(output_json)
def _create_long_amplicon_report(self): """ Creates a Long Amplicon Report """ from pbreports.report.long_amplicon_analysis import run_to_report from test_pbreports_report_long_amplicon_analysis import DATA_DIR as datadir log.info( 'Creating Long Amplicon report using datadir {d}'.format(d=datadir)) input_name = 'amplicon_assembly.csv' file_name = os.path.join(datadir, input_name) report_json = 'long_amplicon.json' output_json = os.path.join(self._output_dir, report_json) report = run_to_report(file_name) pformat(report.to_dict()) report.write_json(output_json) return self._deserialize_report(output_json)