PyDNAnacutil module

A class used for computing different types of DNA descriptors!

You can freely use and distribute it. If you have any problem,

you could contact with us timely.

Authors: Zhijiang Yao and Dongsheng Cao.

Date: 2016.06.14

Email: gadsby@163.com and oriental-cds@163.com

PyDNAnacutil.ComputeBinNum(num_bins, position, k, numbers)[source]
PyDNAnacutil.ComputeQuantileBoundaries(num_bins, k_values, number_filename)[source]
PyDNAnacutil.Diversity(vec)[source]

Calculate diversity.

Parameters:vec – kmer vec
Returns:Diversity(X)
PyDNAnacutil.FindRevcomp(sequence, revcomp_dictionary)[source]
PyDNAnacutil.Frequency(tol_str, tar_str)[source]

Generate the frequency of tar_str in tol_str.

Parameters:
  • tol_str – mother string.
  • tar_str – substring.
PyDNAnacutil.IdXS(vec_x, vec_s, diversity_s)[source]

Calculate ID(X, S)

Parameters:
  • vec_x – kmer X
  • vec_s – kmer S
Returns:

ID(X, S) = Diversity(X + S) - Diversity(X) - Diversity(S)
PyDNAnacutil.MakeIndex(k)[source]
PyDNAnacutil.MakeIndexUptoK(k)[source]
PyDNAnacutil.MakeIndexUptoKRevcomp(k)[source]
PyDNAnacutil.MakeKmerList(k, alphabet)[source]
PyDNAnacutil.MakeKmerVector(seq_list, kmer_list, rev_kmer_list, k, upto, revcomp, normalize)[source]
PyDNAnacutil.MakeRevcompKmerList(kmer_list)[source]
PyDNAnacutil.MakeSequenceVector(sequence, numbers, num_bins, revcomp, revcomp_dictionary, normalize_method, k_values, mismatch, alphabet, kmer_list, boundaries, pseudocount)[source]
PyDNAnacutil.MakeUptoKmerList(k_values, alphabet)[source]
PyDNAnacutil.NormalizeVector(normalize_method, k_values, vector, kmer_list)[source]
PyDNAnacutil.ReadFastaSequence(numeric, fasta_file)[source]
PyDNAnacutil.ReadSequenceAndNumbers(fasta_file, numbers_filename, numbers_file)[source]
PyDNAnacutil.Substitute(position, letter, string)[source]
PyDNAnacutil.cmp(a, b)[source]