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
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 = fofn_to_files(input_fofn)
region_files = fofn_to_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_reads_of_insert_report(self):
"""
Creates and returns a Reads of Insert report.
"""
from pbreports.report.reads_of_insert import fofn_to_files, to_report
from test_pbreports_report_reads_of_insert import _DATA_DIR as datadir
log.info(
'Creating reads_of_insert report using datadir {d}'.format(d=datadir))
bas_files = fofn_to_files(os.path.join(datadir, 'reads_of_insert.fofn'))
output_json = os.path.join(self._output_dir, 'reads_of_insert.json')
report = to_report(bas_files, self._output_dir)
pformat(report.to_dict())
report.write_json(output_json)
return self._deserialize_report(output_json)
def _create_reads_of_insert_report(self):
"""
Creates and returns a Reads of Insert report.
"""
from pbreports.report.reads_of_insert import to_report
from test_pbreports_report_reads_of_insert import _DATA_DIR as datadir
log.info('Creating reads_of_insert report using datadir {d}'.format(
d=datadir))
bas_files = fofn_to_files(os.path.join(datadir,
'reads_of_insert.fofn'))
output_json = os.path.join(self._output_dir, 'reads_of_insert.json')
report = to_report(bas_files, self._output_dir)
pformat(report.to_dict())
report.write_json(output_json)
return self._deserialize_report(output_json)
def _create_filter_subread_report(self):
"""
Creates and returns a Filter Subreads report
"""
from pbreports.report.filter_subread import to_report
from test_pbreports_report_filter_subread import ROOT_DATA_DIR, _DATA_DIR_NAME
datadir = os.path.join(ROOT_DATA_DIR, _DATA_DIR_NAME)
log.info('Creating Filter subreads report using datadir {d}'.format(
d=datadir))
output_name = 'filter_subread.json'
filtered_summary = os.path.join(datadir,
'filtered_subread_summary.csv')
output_json = os.path.join(self._output_dir, output_name)
report = to_report(filtered_summary, self._output_dir)
pformat(report)
report.write_json(output_json)
return self._deserialize_report(output_json)
def _create_filter_subread_report(self):
"""
Creates and returns a Filter Subreads report
"""
from pbreports.report.filter_subread import to_report
from test_pbreports_report_filter_subread import ROOT_DATA_DIR, _DATA_DIR_NAME
datadir = os.path.join(ROOT_DATA_DIR, _DATA_DIR_NAME)
log.info(
'Creating Filter subreads report using datadir {d}'.format(d=datadir))
output_name = 'filter_subread.json'
filtered_summary = os.path.join(
datadir, 'filtered_subread_summary.csv')
output_json = os.path.join(self._output_dir, output_name)
report = to_report(filtered_summary, self._output_dir)
pformat(report)
report.write_json(output_json)
return self._deserialize_report(output_json)
def _create_preassembly_report(self):
"""
Creates and returns a Preassembly report.
"""
from pbreports.report.preassembly import to_report
from test_pbreports_report_preassembler import _DATA_DIR as datadir
log.info(
'Creating preassembly report using datadir {d}'.format(d=datadir))
filtered_reads = os.path.join(datadir, 'filtered_subreads.fasta')
filtered_longreads = os.path.join(datadir, 'filtered_longreads.fasta')
corrected_reads = os.path.join(datadir, 'corrected.fasta')
output_json = os.path.join(self._output_dir, 'preassembly_report.json')
length_cutoff = 6000
report = to_report(
filtered_reads, filtered_longreads, corrected_reads, length_cutoff=None)
pformat(report.to_dict())
report.write_json(output_json)
return self._deserialize_report(output_json)
def _create_preassembly_report(self):
"""
Creates and returns a Preassembly report.
"""
from pbreports.report.preassembly import to_report
from test_pbreports_report_preassembler import _DATA_DIR as datadir
log.info(
'Creating preassembly report using datadir {d}'.format(d=datadir))
filtered_reads = os.path.join(datadir, 'filtered_subreads.fasta')
filtered_longreads = os.path.join(datadir, 'filtered_longreads.fasta')
corrected_reads = os.path.join(datadir, 'corrected.fasta')
output_json = os.path.join(self._output_dir, 'preassembly_report.json')
length_cutoff = 6000
report = to_report(filtered_reads,
filtered_longreads,
corrected_reads,
length_cutoff=None)
pformat(report.to_dict())
report.write_json(output_json)
return self._deserialize_report(output_json)