def create_command(module_type):
cmd_dict = get_cmd_spec(module_type)
vars, inner_cmd = cmd_dict['vars'], cmd_dict['inner_cmd']
cmd_opts = dictzip(vars, map(getvar, vars))
if module_type != None:
whole_cmd = wrap_cmd(module_type, inner_cmd)
return whole_cmd.format(**cmd_opts)
else:
return inner_cmd
def create_command(module_type):
cmd_dict = get_cmd_spec(module_type)
vars, inner_cmd = cmd_dict['vars'], cmd_dict['inner_cmd']
cmd_opts = dictzip(vars, map(getvar, vars))
if module_type != None:
whole_cmd = wrap_cmd(module_type, inner_cmd)
return whole_cmd.format(**cmd_opts)
else:
return inner_cmd
def _create_dict(obj_func, columns, getters, validator, dictgetters):
obj = apply(obj_func)
pre_dict = obj_to_dict(obj, dictzip(columns, getters))
#optional intermediate schema here
if dictgetters:
extra_dict = obj_to_dict(pre_dict, dictgetters)
full_dict = merge_dicts(pre_dict, extra_dict)
else:
full_dict = pre_dict
return validator.validate(full_dict)
def _create_dict(obj_func, columns, getters, validator, dictgetters):
obj = apply(obj_func)
pre_dict = obj_to_dict(obj, dictzip(columns, getters))
#optional intermediate schema here
if dictgetters:
extra_dict = obj_to_dict(pre_dict, dictgetters)
full_dict = merge_dicts(pre_dict, extra_dict)
else:
full_dict = pre_dict
return validator.validate(full_dict)
def make_ovrlp_graph(kmers):
N = len(kmers)
ov = len(kmers[0]) - 1
M = np.zeros((N, N))
D = dictzip(kmers, xrange(N))
def update(M, pre, suff):
sfx, suffg = suff
nbrs = imap(X[0], ifilter(X[1]==sfx, pre))
nbr_idxs = map(D.__getitem__, nbrs)
s_idxs = map(D.__getitem__, suffg)
M[ s_idxs, nbr_idxs] = 1
pre, suff = groupby(kmers, X[:ov]), groupby(kmers, X[-ov:])
pre = izip(kmers, imap(X[:ov], kmers))
Mupdate = F(update, M, pre)
#NOTE: starmap drains itertools.groupby
map(Mupdate, suff)
return D, M
def make_job_dict():
modules = get_available_modules() + ['Other']
module_type = select_interactive_menu(modules)
pbs_opts = dictzip(opts, map(option_with_default, opts))
pbs_opts['command'] = create_command(module_type)
return pbs_opts
def make_job_dict():
modules = get_available_modules() + ['Other']
module_type = select_interactive_menu(modules)
pbs_opts = dictzip(opts, map(option_with_default, opts))
pbs_opts['command'] = create_command(module_type)
return pbs_opts