def acc(input_data,
k,
lag,
phyche_list,
alphabet,
extra_index_file=None,
all_prop=False,
theta_type=1):
"""This is a complete acc in PseKNC.
:param k: int, the value of k-tuple.
:param phyche_list: list, the input physicochemical properties list.
:param extra_index_file: a file path includes the user-defined phyche_index.
:param all_prop: bool, choose all physicochemical properties or not.
:param theta_type: the value 1, 2 and 3 for ac, cc or acc.
"""
phyche_list = get_phyche_list(k,
phyche_list,
extra_index_file=extra_index_file,
alphabet=alphabet,
all_prop=all_prop)
# print(phyche_list)
# Get phyche_vals.
if alphabet == index_list.DNA or alphabet == index_list.RNA:
if extra_index_file is not None:
extra_phyche_index = get_extra_index(extra_index_file)
from util import normalize_index
phyche_vals = get_phyche_value(
k, phyche_list, alphabet,
normalize_index(extra_phyche_index,
alphabet,
is_convert_dict=True))
else:
phyche_vals = get_phyche_value(k, phyche_list, alphabet)
elif alphabet == index_list.PROTEIN:
phyche_vals = get_aaindex(phyche_list)
# print(phyche_vals)
if extra_index_file is not None:
phyche_vals.extend(extend_aaindex(extra_index_file))
seqs = get_data(input_data, alphabet)
if alphabet == index_list.PROTEIN:
# Transform the data format to dict {acid: [phyche_vals]}.
phyche_keys = phyche_vals[0].index_dict.keys()
phyche_vals = [e.index_dict.values() for e in phyche_vals]
new_phyche_vals = zip(*[e for e in phyche_vals])
phyche_vals = {
key: list(val)
for key, val in zip(phyche_keys, new_phyche_vals)
}
if theta_type == 1:
return make_ac_vec(seqs, lag, phyche_vals, k)
elif theta_type == 2:
return make_cc_vec(seqs, lag, phyche_vals, k)
elif theta_type == 3:
return make_acc_vec(seqs, lag, phyche_vals, k)
def acc(input_data, k, lag, phyche_list, alphabet, extra_index_file=None, all_prop=False, theta_type=1):
"""This is a complete acc in PseKNC.
:param k: int, the value of k-tuple.
:param phyche_list: list, the input physicochemical properties list.
:param extra_index_file: a file path includes the user-defined phyche_index.
:param all_prop: bool, choose all physicochemical properties or not.
:param theta_type: the value 1, 2 and 3 for ac, cc or acc.
"""
phyche_list = get_phyche_list(
k, phyche_list, extra_index_file=extra_index_file, alphabet=alphabet, all_prop=all_prop
)
# print(phyche_list)
# Get phyche_vals.
if alphabet == index_list.DNA or alphabet == index_list.RNA:
if extra_index_file is not None:
extra_phyche_index = get_extra_index(extra_index_file)
from util import normalize_index
phyche_vals = get_phyche_value(
k, phyche_list, alphabet, normalize_index(extra_phyche_index, alphabet, is_convert_dict=True)
)
else:
phyche_vals = get_phyche_value(k, phyche_list, alphabet)
elif alphabet == index_list.PROTEIN:
phyche_vals = get_aaindex(phyche_list)
# print(phyche_vals)
if extra_index_file is not None:
phyche_vals.extend(extend_aaindex(extra_index_file))
seqs = get_data(input_data, alphabet)
if alphabet == index_list.PROTEIN:
# Transform the data format to dict {acid: [phyche_vals]}.
phyche_keys = phyche_vals[0].index_dict.keys()
phyche_vals = [e.index_dict.values() for e in phyche_vals]
new_phyche_vals = zip(*[e for e in phyche_vals])
phyche_vals = {key: list(val) for key, val in zip(phyche_keys, new_phyche_vals)}
if theta_type == 1:
return make_ac_vec(seqs, lag, phyche_vals, k)
elif theta_type == 2:
return make_cc_vec(seqs, lag, phyche_vals, k)
elif theta_type == 3:
return make_acc_vec(seqs, lag, phyche_vals, k)