Beispiel #1
0
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'))
Beispiel #5
0
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)
Beispiel #6
0
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)