示例#1
0
    def _create_overview_report(self):
        """
        Creates and returns an Overview report
        """
        from pbreports.report.overview import run
        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 = fofn_to_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)
    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)
示例#3
0
 def setUp(self):
     self.input_file = pbtestdata.get_file("subreads-xml")
     self.report = overview.run(self.input_file)
     log.info(pformat(self.report.to_dict()))
 def setUp(self):
     self.input_file = op.join(ROOT_DATA_DIR, "dacetoxidans", "2530923",
                               "0005_0006.subreadset.xml")
     self.report = overview.run(self.input_file)
     log.info(pformat(self.report.to_dict()))
 def setUp(self):
     self.input_file = op.join(ROOT_DATA_DIR, "dacetoxidans", "2530923",
                               "0005_0006.subreadset.xml")
     self.report = overview.run(self.input_file)
     log.info(pformat(self.report.to_dict()))