Source code for easy_dna.random_sequences

"""Methods to generate random sequences.

Also see utils.random_compatible_sequence() for random sequences verifying
user-provided constraints.
"""

import numpy as np




def random_dna_sequence(length, gc_share=None, probas=None, seed=None):
    """Return a random DNA sequence ("ATGGCGT...") with the specified length.

    Parameters
    ----------
    length : int
        Length of the DNA sequence.
    gc_share : float, optional
        The GC content of the random sequence, as a fraction (for example, 0.3 for 30%).
        Overwrites `probas`.
    probas : dict, optional
        Frequencies for the different nucleotides, for instance
        `probas={"A":0.2, "T":0.3, "G":0.3, "C":0.2}`.
        If not specified, all nucleotides are equiprobable (p=0.25).
    seed : int, optional
        The seed to feed to the random number generator. When a seed is provided,
        the random results depend deterministically on the seed, thus enabling
        reproducibility.
    """
    if seed is not None:
        np.random.seed(seed)
    if gc_share is not None:
        g_or_c = gc_share / 2.0
        not_g_or_c = (1 - gc_share) / 2.0
        probas = {"G": g_or_c, "C": g_or_c, "A": not_g_or_c, "T": not_g_or_c}
    if probas is None:
        sequence = np.random.choice(list("ATCG"), length)
    else:
        bases, probas = zip(*probas.items())
        sequence = np.random.choice(bases, length, p=probas)
    return "".join(sequence)





def random_protein_sequence(length, seed=None):
    """Return a random protein sequence "MNQTW...YL*" of the specified length.

    Parameters
    ----------
    length : int
        Length of the protein sequence (in number of amino acids). Note that the
        sequence will always start with "M" and end with a stop codon "*"
        with (length-2) random amino acids in the middle.
    seed : int, optional
        The seed to feed to the random number generator. When a seed is provided,
        the random results depend deterministically on the seed, thus enabling
        reproducibility.
    """
    if seed is not None:
        np.random.seed(seed)

    aa_list = list("ACEDGFIHKLNQPSRTWVY")
    aa_choices = np.random.choice(aa_list, length - 2)
    return "M" + "".join(aa_choices) + "*"