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_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)
