test_basics.py 文件源码

def test_plot_with_gc_content(tmpdir):

    fig, (ax1, ax2) = plt.subplots(2, 1, figsize=(8, 4), sharex=True)

    # Parse the genbank file, plot annotations
    record = SeqIO.read(example_genbank, "genbank")
    graphic_record = BiopythonTranslator().translate_record(record)
    ax, levels = graphic_record.plot()
    graphic_record.plot(ax=ax1, with_ruler=False)

    # Plot the local GC content
    def plot_local_gc_content(record, window_size, ax):
        def gc_content(seq):
            return 100.0*len([c for c in seq if c in "GC"]) / len(seq)
        yy = [gc_content(record.seq[i:i+window_size])
              for i in range(len(record.seq)-window_size)]
        xx = np.arange(len(record.seq)-window_size)+25
        ax.fill_between(xx, yy, alpha=0.3)
        ax.set_ylabel("GC(%)")

    plot_local_gc_content(record, window_size=50, ax=ax2)

    # Resize the figure to the right height
    target_file = os.path.join(str(tmpdir), "with_plot.png")
    fig.tight_layout()
    fig.savefig(target_file)