def for_task( i_length_cutoff_fn, i_json_config_fn, i_preads_fofn_fn, i_raw_reads_db_fn, # maybe symlinked o_json_fn, ): """This is used by HGAP4, run_report_preassembly_yield(). See pbfalcon.tusks """ tasks_dir = os.path.dirname(os.path.dirname(i_json_config_fn)) cfg = _get_cfg(i_json_config_fn, i_length_cutoff_fn) genome_length = int(cfg.get('genome_size', 0)) # different name in falcon length_cutoff = cfg['length_cutoff'] i_raw_reads_db_fn = os.path.realpath(i_raw_reads_db_fn) report_dict = stats_preassembly.calc_dict( i_preads_fofn_fn, i_raw_reads_db_fn, genome_length, length_cutoff, ) report = produce_report(**report_dict) with open(o_json_fn, 'w') as ofs: log.info("Writing report to {!r}:\n{}".format(o_json_fn, report)) ofs.write(report)
def for_task( i_json_config_fn, i_preads_fofn_fn, i_raw_reads_db_fn, # maybe symlinked o_json_fn, ): """See pbfalcon.tusks """ tasks_dir = os.path.dirname(os.path.dirname(i_json_config_fn)) i_length_cutoff_fn = os.path.join(tasks_dir, 'falcon_ns.tasks.task_falcon0_build_rdb-0', 'length_cutoff') cfg = _get_cfg(i_json_config_fn, i_length_cutoff_fn) genome_length = int(cfg.get('genome_size', 0)) # different name in falcon length_cutoff = cfg['length_cutoff'] i_raw_reads_db_fn = os.path.realpath(i_raw_reads_db_fn) report_dict = stats_preassembly.calc_dict( i_preads_fofn_fn, i_raw_reads_db_fn, genome_length, length_cutoff, ) report = produce_report(**report_dict) log.info('%r -> %r' %(report, o_json_fn)) with open(o_json_fn, 'w') as ofs: log.info("Writing report to {!r}.".format(o_json_fn)) content = report.to_json() ofs.write(content)
def task_report_pre_assembly(self): # TODO(CD): Bashify this, in case it is slow. i_raw_reads_db_fn = fn(self.raw_reads_db) i_preads_fofn_fn = fn(self.preads_fofn) i_length_cutoff_fn = fn(self.length_cutoff_fn) o_json_fn = fn(self.pre_assembly_report) cfg = self.parameters genome_length = int(cfg.get('genome_size', 0)) # different name in falcon length_cutoff = int(cfg['length_cutoff']) length_cutoff = support.get_length_cutoff(length_cutoff, i_length_cutoff_fn) kwds = { 'i_raw_reads_db_fn': i_raw_reads_db_fn, 'i_preads_fofn_fn': i_preads_fofn_fn, 'genome_length': genome_length, 'length_cutoff': length_cutoff, } fc_run_logger.info('Report inputs: {}'.format(repr(kwds))) report_dict = stats_preassembly.calc_dict(**kwds) content = json.dumps(report_dict, sort_keys=True, indent=4, separators=(',', ': ')) fc_run_logger.info('Report stats:\n{}'.format(content)) open(o_json_fn, 'w').write(content)
def for_task( i_json_config_fn, i_preads_fofn_fn, i_raw_reads_db_fn, # maybe symlinked o_json_fn, ): """This is used by HGAP4, run_report_preassembly_yield(). See pbfalcon.tusks """ tasks_dir = os.path.dirname(os.path.dirname(i_json_config_fn)) i_length_cutoff_fn = os.path.join(tasks_dir, 'falcon_ns.tasks.task_falcon0_build_rdb-0', 'length_cutoff') cfg = _get_cfg(i_json_config_fn, i_length_cutoff_fn) genome_length = int(cfg.get('genome_size', 0)) # different name in falcon length_cutoff = cfg['length_cutoff'] i_raw_reads_db_fn = os.path.realpath(i_raw_reads_db_fn) report_dict = stats_preassembly.calc_dict( i_preads_fofn_fn, i_raw_reads_db_fn, genome_length, length_cutoff, ) report = produce_report(**report_dict) with open(o_json_fn, 'w') as ofs: log.info("Writing report to {!r}:\n{}".format(o_json_fn, report)) ofs.write(report)