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