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)
Example #2
0
    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)
Example #4
0
    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)