def _create_mapping_stats_gmap_report(self): """ Creates and returns a Mapping Stats gmap report """ from pbreports.report.mapping_stats import to_report, bas_fofn_to_bas_files from test_pbreports_report_mapping_stats import _GMAP_DATA_DIR as datadir log.info( 'Creating Mapping Stats gmap report using datadir {d}'.format(d=datadir)) _to_p = lambda x: os.path.join(datadir, x) filtered_regions_fofn = _to_p('filtered_regions.fofn') filtered_summary = _to_p('filtered_summary.csv') input_fofn = _to_p('input.fofn') aligned_reads_cmph5 = _to_p('aligned_reads.cmp.h5') mode = "external" report_json = 'mapping_report.json' output_json = os.path.join(self._output_dir, 'mapping_report.json') bas_files = bas_fofn_to_bas_files(input_fofn) region_files = bas_fofn_to_bas_files(filtered_regions_fofn) report = to_report(bas_files, region_files, aligned_reads_cmph5, report_json, self._output_dir, filter_summary_csv=filtered_summary, mode=mode) pformat(report.to_dict()) report.write_json(output_json) return self._deserialize_report(output_json)
def _create_mapping_stats_gmap_report(self): """ Creates and returns a Mapping Stats gmap report """ from pbreports.report.mapping_stats import to_report, bas_fofn_to_bas_files from test_pbreports_report_mapping_stats import _GMAP_DATA_DIR as datadir log.info('Creating Mapping Stats gmap report using datadir {d}'.format( d=datadir)) _to_p = lambda x: os.path.join(datadir, x) filtered_regions_fofn = _to_p('filtered_regions.fofn') filtered_summary = _to_p('filtered_summary.csv') input_fofn = _to_p('input.fofn') aligned_reads_cmph5 = _to_p('aligned_reads.cmp.h5') mode = "external" report_json = 'mapping_report.json' output_json = os.path.join(self._output_dir, 'mapping_report.json') bas_files = bas_fofn_to_bas_files(input_fofn) region_files = bas_fofn_to_bas_files(filtered_regions_fofn) report = to_report(bas_files, region_files, aligned_reads_cmph5, report_json, self._output_dir, filter_summary_csv=filtered_summary, mode=mode) pformat(report.to_dict()) report.write_json(output_json) return self._deserialize_report(output_json)
def _create_overview_report(self): """ Creates and returns an Overview report """ from pbreports.report.overview import run, bas_fofn_to_bas_files from test_pbreports_report_overview import _DATA_DIR as datadir log.info( 'Creating Overview report using datadir {d}'.format(d=datadir)) input_name = 'input.fofn' input_fofn = os.path.join(datadir, input_name) bas_files = bas_fofn_to_bas_files(input_fofn) report_json = 'overview.json' output_json = os.path.join(self._output_dir, report_json) report = run(bas_files) pformat(report.to_dict()) report.write_json(output_json) return self._deserialize_report(output_json)