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)
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()))