def _get_cfg(i_json_config_fn, i_length_cutoff_fn):
cfg = json.loads(stricter_json(open(i_json_config_fn).read()))
log.info('cfg=\n%s' % pprint.pformat(cfg))
length_cutoff = int(cfg.get('length_cutoff', '0'))
length_cutoff = get_length_cutoff(length_cutoff, i_length_cutoff_fn)
cfg['length_cutoff'] = length_cutoff
return cfg
def _get_cfg(i_json_config_fn, i_length_cutoff_fn):
cfg = json.loads(stricter_json(open(i_json_config_fn).read()))
log.info('cfg=\n%s' %pprint.pformat(cfg))
length_cutoff = int(cfg.get('length_cutoff', '0'))
length_cutoff = get_length_cutoff(length_cutoff, i_length_cutoff_fn)
cfg['length_cutoff'] = length_cutoff
return cfg
def run_hgap_prepare(input_files, output_files, options):
"""Generate a config-file from options.
"""
say('options to run_hgap_prepare:\n{}'.format(pprint.pformat(options)))
i_subreadset_fn, = input_files
o_hgap_cfg_fn, o_logging_cfg_fn, o_log_fn = output_files
run_dir = os.path.dirname(o_hgap_cfg_fn)
symlink(os.path.join(run_dir, 'stderr'), o_log_fn)
# This will be the cfg we pass to hgap_run.
all_cfg = collections.defaultdict(lambda: collections.defaultdict(str))
# Get grid options, for job-distribution.
update_for_grid(all_cfg, run_dir)
# Set some other falcon options, based on hgap options.
update_falcon(all_cfg)
# Override from pbsmrtpipe config/preset.xml.
all_cfg[OPTION_SECTION_FALCON]['genome_size'] = options[
TASK_HGAP_GENOME_LENGTH].strip()
all_cfg[OPTION_SECTION_FALCON]['length_cutoff'] = options[
TASK_HGAP_SEED_LENGTH_CUTOFF].strip()
all_cfg[OPTION_SECTION_FALCON]['seed_coverage'] = options[
TASK_HGAP_SEED_COVERAGE].strip()
cfg_json = options[TASK_HGAP_OPTIONS].strip()
if not cfg_json:
cfg_json = '{}'
override_cfg = json.loads(stricter_json(cfg_json))
update2(all_cfg, override_cfg)
# Get options from pbsmrtpipe.
pbsmrtpipe_opts = get_pbsmrtpipe_opts(run_dir)
if OPTION_SECTION_PBSMRTPIPE not in all_cfg:
all_cfg[OPTION_SECTION_PBSMRTPIPE] = dict()
pbsmrtpipe_opts.update(all_cfg[OPTION_SECTION_PBSMRTPIPE])
all_cfg[OPTION_SECTION_PBSMRTPIPE] = pbsmrtpipe_opts
# Dump all_cfg.
say('Dumping to {}'.format(repr(o_hgap_cfg_fn)))
dump_as_json(all_cfg, open(o_hgap_cfg_fn, 'w'))
# Get logging cfg.
logging_cfg = DEFAULT_LOGGING_CFG
# Dump logging cfg.
say('Dumping to {}'.format(repr(o_logging_cfg_fn)))
dump_as_json(logging_cfg, open(o_logging_cfg_fn, 'w'))
def run_hgap_prepare(input_files, output_files, options):
"""Generate a config-file from options.
"""
say('options to run_hgap_prepare:\n{}'.format(pprint.pformat(options)))
i_subreadset_fn, = input_files
o_hgap_cfg_fn, o_logging_cfg_fn, o_log_fn = output_files
run_dir = os.path.dirname(o_hgap_cfg_fn)
symlink(os.path.join(run_dir, 'stderr'), o_log_fn)
# This will be the cfg we pass to hgap_run.
all_cfg = collections.defaultdict(lambda: collections.defaultdict(str))
# Get grid options, for job-distribution.
update_for_grid(all_cfg, run_dir)
# Set some other falcon options, based on hgap options.
update_falcon(all_cfg)
# Override from pbsmrtpipe config/preset.xml.
all_cfg[OPTION_SECTION_FALCON]['genome_size'] = options[TASK_HGAP_GENOME_LENGTH].strip()
all_cfg[OPTION_SECTION_FALCON]['length_cutoff'] = options[TASK_HGAP_SEED_LENGTH_CUTOFF].strip()
all_cfg[OPTION_SECTION_FALCON]['seed_coverage'] = options[TASK_HGAP_SEED_COVERAGE].strip()
cfg_json = options[TASK_HGAP_OPTIONS].strip()
if not cfg_json:
cfg_json = '{}'
override_cfg = json.loads(stricter_json(cfg_json))
update2(all_cfg, override_cfg)
update_pwatcher(all_cfg)
# Get options from pbsmrtpipe.
pbsmrtpipe_opts = get_pbsmrtpipe_opts(run_dir)
if OPTION_SECTION_PBSMRTPIPE not in all_cfg:
all_cfg[OPTION_SECTION_PBSMRTPIPE] = dict()
pbsmrtpipe_opts.update(all_cfg[OPTION_SECTION_PBSMRTPIPE])
all_cfg[OPTION_SECTION_PBSMRTPIPE] = pbsmrtpipe_opts
# Dump all_cfg.
say('Dumping to {}'.format(repr(o_hgap_cfg_fn)))
dump_as_json(all_cfg, open(o_hgap_cfg_fn, 'w'))
# Get logging cfg.
logging_cfg = DEFAULT_LOGGING_CFG
# Dump logging cfg.
say('Dumping to {}'.format(repr(o_logging_cfg_fn)))
dump_as_json(logging_cfg, open(o_logging_cfg_fn, 'w'))
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):
stats = json.loads(stricter_json(stats_ifs.read()))
report = produce_report(**stats)
content = report.to_json()
report_ofs.write(content)
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)
