def args_runner(args):
# UNTESTED -- and needs update for DAZZ_DB -- but never used anyway
log.info("Starting {f}".format(f=os.path.basename(__file__)))
filtered_subreads = args.filtered_subreads_fasta
filtered_longreads = args.filtered_longreads_fasta #???
corrected_reads = args.corrected_reads
length_cutoff = args.length_cutoff
genome_length = args.genome_length
output_json = args.output_json
cfg = {
'length_cutoff': length_cutoff,
}
report_dict = stats_preassembly.make_dict(
corrected_reads,
filtered_subreads,
genome_length,
length_cutoff,
)
report = produce_report(**report_dict)
log.info(report)
with open(output_json, 'w') as f:
log.info("Writing report to {!r}.".format(output_json))
f.write(report)
return 0
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 args_runner(args):
# UNTESTED -- and needs update for DAZZ_DB -- but never used anyway
log.info("Starting {f}".format(f=os.path.basename(__file__)))
filtered_subreads = args.filtered_subreads_fasta
filtered_longreads = args.filtered_longreads_fasta #???
corrected_reads = args.corrected_reads
length_cutoff = args.length_cutoff
genome_length = args.genome_length
output_json = args.output_json
cfg = {
'length_cutoff': length_cutoff,
}
report_dict = falcon_polish.stats_preassembly.make_dict(
corrected_reads,
filtered_subreads,
genome_length,
length_cutoff,
)
report = produce_report(**report_dict)
log.info(report)
with open(output_json, 'w') as f:
log.info("Writing report to {!r}.".format(output_json))
f.write(report)
return 0
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)
def write_report_from_stats(stats_ifs, report_ofs):
"""This is used by HGAP5, task_run_hgap.py.
"""
stats = json.loads(stricter_json(stats_ifs.read()))
report = produce_report(**stats)
report_ofs.write(report)
def write_report_from_stats(stats_ifs, report_ofs):
"""This is used by HGAP5, task_run_hgap.py.
"""
stats = json.loads(stricter_json(stats_ifs.read()))
report = produce_report(**stats)
report_ofs.write(report)
