def get_phyche_index(k, phyche_list, alphabet):
"""get phyche_value according phyche_list."""
phyche_value = {}
if 0 == len(phyche_list):
for nucleotide in make_kmer_list(k, alphabet):
phyche_value[nucleotide] = []
return phyche_value
nucleotide_phyche_value = get_phyche_factor_dic(k, alphabet)
for nucleotide in make_kmer_list(k, alphabet):
if nucleotide not in phyche_value:
phyche_value[nucleotide] = []
for e in nucleotide_phyche_value[nucleotide]:
if e[0] in phyche_list:
phyche_value[nucleotide].append(e[1])
return phyche_value
def get_phyche_index(k, phyche_list, alphabet):
"""get phyche_value according phyche_list."""
phyche_value = {}
if 0 == len(phyche_list):
for nucleotide in make_kmer_list(k, alphabet):
phyche_value[nucleotide] = []
return phyche_value
nucleotide_phyche_value = get_phyche_factor_dic(k, alphabet)
for nucleotide in make_kmer_list(k, alphabet):
if nucleotide not in phyche_value:
phyche_value[nucleotide] = []
for e in nucleotide_phyche_value[nucleotide]:
if e[0] in phyche_list:
phyche_value[nucleotide].append(e[1])
return phyche_value
def make_pseknc_vector(sequence_list,
phyche_value,
k=2,
w=0.05,
lamada=1,
alphabet=index_list.DNA,
theta_type=1):
"""Generate the pseknc vector."""
kmer = make_kmer_list(k, alphabet)
vector = []
for sequence in sequence_list:
if len(sequence) < k or lamada + k > len(sequence):
error_info = "Sorry, the sequence length must be larger than " + str(
lamada + k)
sys.stderr.write(error_info)
sys.exit(0)
# Get the nucleotide frequency in the DNA sequence.
fre_list = [frequency(sequence, str(key)) for key in kmer]
fre_sum = float(sum(fre_list))
# Get the normalized occurrence frequency of nucleotide in the DNA sequence.
fre_list = [e / fre_sum for e in fre_list]
# Get the theta_list.
if 1 == theta_type:
theta_list = get_parallel_factor(k, lamada, sequence, phyche_value,
alphabet)
elif 2 == theta_type:
theta_list = get_series_factor(k, lamada, sequence, phyche_value,
alphabet)
elif 3 == theta_type:
theta_list = get_parallel_factor(k=2,
lamada=lamada,
sequence=sequence,
phyche_value=phyche_value,
alphabet=alphabet)
theta_sum = sum(theta_list)
# Generate the vector according the Equation 9.
denominator = 1 + w * theta_sum
temp_vec = [round(f / denominator, 8) for f in fre_list]
for theta in theta_list:
temp_vec.append(round(w * theta / denominator, 8))
vector.append(temp_vec)
return vector
def gen_vector(tng_list, n):
"""Generate feature vectors based on the top-n-gram.
:param tng_list: the generated top-n-gram list.
:param n: the n most frequent amino acids in the amino acid frequency profiles.
"""
gram_list = make_kmer_list(n, const.PROTEIN)
#print tng_list
#print gram_list
vector_list = []
for tng in tng_list:
vec_len = len(tng)
#print vec_len
vector = []
for elem in gram_list:
gram_count = tng.count(elem)
occur_freq = round((gram_count * 1.0) / vec_len, 4)
vector.append(occur_freq)
vector_list.append(vector)
return vector_list
def make_pseknc_vector(sequence_list, phyche_value, k=2, w=0.05, lamada=1, alphabet=index_list.DNA, theta_type=1):
"""Generate the pseknc vector."""
kmer = make_kmer_list(k, alphabet)
vector = []
for sequence in sequence_list:
if len(sequence) < k or lamada + k > len(sequence):
error_info = "Sorry, the sequence length must be larger than " + str(lamada + k)
sys.stderr.write(error_info)
sys.exit(0)
# Get the nucleotide frequency in the DNA sequence.
fre_list = [frequency(sequence, str(key)) for key in kmer]
fre_sum = float(sum(fre_list))
# Get the normalized occurrence frequency of nucleotide in the DNA sequence.
fre_list = [e / fre_sum for e in fre_list]
# Get the theta_list.
if 1 == theta_type:
theta_list = get_parallel_factor(k, lamada, sequence, phyche_value, alphabet)
elif 2 == theta_type:
theta_list = get_series_factor(k, lamada, sequence, phyche_value, alphabet)
elif 3 == theta_type:
theta_list = get_parallel_factor(k=2, lamada=lamada, sequence=sequence,
phyche_value=phyche_value, alphabet=alphabet)
theta_sum = sum(theta_list)
# Generate the vector according the Equation 9.
denominator = 1 + w * theta_sum
temp_vec = [round(f / denominator, 8) for f in fre_list]
for theta in theta_list:
temp_vec.append(round(w * theta / denominator, 8))
vector.append(temp_vec)
return vector