Ejemplo n.º 1
0
def run_falcon_config_get_fasta(input_files, output_files):
    i_config_fn, = input_files
    o_fofn_fn, = output_files
    config = _get_config(i_config_fn)
    i_fofn_fn = config['input_fofn']
    if not os.path.isabs(i_fofn_fn):
        i_fofn_fn = os.path.join(os.path.dirname(i_config_fn), i_fofn_fn)
    msg = '%r -> %r' % (i_fofn_fn, o_fofn_fn)
    say(msg)
    with cd(os.path.dirname(i_fofn_fn)):
        support.make_fofn_abs(i_fofn_fn, o_fofn_fn)
Ejemplo n.º 2
0
def run_falcon_config_get_fasta(input_files, output_files):
        i_config_fn, = input_files
        o_fofn_fn, = output_files
        config = _get_config(i_config_fn)
        i_fofn_fn = config['input_fofn_fn']
        msg = '%r -> %r' %(i_fofn_fn, o_fofn_fn)
        say(msg)
        with cd(os.path.dirname(i_fofn_fn)):
            return support.make_fofn_abs(i_fofn_fn, o_fofn_fn)
Ejemplo n.º 3
0
def run_falcon_config_get_fasta(input_files, output_files):
    i_config_fn, = input_files
    o_fofn_fn, = output_files
    config = _get_config(i_config_fn)
    i_fofn_fn = config["input_fofn"]
    if not os.path.isabs(i_fofn_fn):
        i_fofn_fn = os.path.join(os.path.dirname(i_config_fn), i_fofn_fn)
    msg = "%r -> %r" % (i_fofn_fn, o_fofn_fn)
    say(msg)
    with cd(os.path.dirname(i_fofn_fn)):
        return support.make_fofn_abs(i_fofn_fn, o_fofn_fn)
    return 0
Ejemplo n.º 4
0
def run_falcon_make_fofn_abs(input_files, output_files):
        i_json_fn, = input_files
        o_fofn_fn, = output_files
        config = _get_config_from_json_fileobj(open(i_json_fn))
        i_fofn_fn = config['input_fofn_fn']
        if not i_fofn_fn.startswith('/'):
            # i_fofn_fn can be relative to the location of the config file.
            original_config_fn = config['ORIGINAL_SELF']
            i_fofn_fn = os.path.join(os.path.dirname(original_config_fn), i_fofn_fn)
        msg = 'run_falcon_make_fofn_abs(%r -> %r)' %(i_fofn_fn, o_fofn_fn)
        say(msg)
        with cd(os.path.dirname(i_fofn_fn)):
            return support.make_fofn_abs(i_fofn_fn, o_fofn_fn)
Ejemplo n.º 5
0
def run_falcon_make_fofn_abs(input_files, output_files):
    i_json_fn, = input_files
    o_fofn_fn, = output_files
    config = _get_config_from_json_fileobj(open(i_json_fn))
    i_fofn_fn = config['input_fofn']
    if not i_fofn_fn.startswith('/'):
        # i_fofn_fn can be relative to the location of the config file.
        original_config_fn = config['original_self']
        i_fofn_fn = os.path.join(os.path.dirname(original_config_fn),
                                 i_fofn_fn)
    msg = 'run_falcon_make_fofn_abs(%r -> %r)' % (i_fofn_fn, o_fofn_fn)
    say(msg)
    with cd(os.path.dirname(i_fofn_fn)):
        return support.make_fofn_abs(i_fofn_fn, o_fofn_fn)
    return 0