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)