Visualize a list of sequences (of same length, assuming DNA encoding) as a color coded matrix

viz_seq.py

import pylab
import numpy


def show_seqs(seqs):
    """
    plot color coded training sequences
    """


    pylab.figure()


    num_seqs = len(seqs)
    len_seqs = len(seqs[0])

    color_matrix = numpy.zeros((num_seqs, len_seqs))

    base_map= {"A": 0, "T": 1, "G": 2, "C": 3}

    for i, seq in enumerate(seqs):
        for j, nucl in enumerate(seq):
            color_matrix[i,j] = base_map[nucl]

    pylab.imshow(color_matrix)

    # add a 'best fit' line
    #y = mlab.normpdf( bins, mu, sigma)
    #l = pylab.plot(bins, y, 'r--', linewidth=1)
    pylab.title("seqs distribution")
    pylab.xlabel("seq pos")
    pylab.ylabel("seq")


    pylab.show()