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)
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)
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
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)
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