コード例 #1
0
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
コード例 #2
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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
コード例 #3
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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
コード例 #4
0
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