def test_plot_with_bokeh(tmpdir): gb_record = SeqIO.read(example_genbank, "genbank") record = BiopythonTranslator().translate_record(record=gb_record) plot = record.plot_with_bokeh(figure_width=8) target_file = os.path.join(str(tmpdir), "plot_with_bokeh.html") with open(target_file, "w+") as f: f.write(file_html(plot, CDN, "Example Sequence")) with open(target_file, "r") as f: assert len(f.read()) > 5000
def test_plot_with_bokeh_no_labels(tmpdir): """Bokeh has a problem with empty lists of labels.""" gb_record = SeqIO.read(example_genbank, "genbank") record = BiopythonTranslator().translate_record(record=gb_record) for feature in record.features: feature.label = None plot = record.plot_with_bokeh(figure_width=8) target_file = os.path.join(str(tmpdir), "plot_with_bokeh.html") with open(target_file, "w+") as f: f.write(file_html(plot, CDN, "Example Sequence")) with open(target_file, "r") as f: assert len(f.read()) > 5000
"""Simple example with Bokeh output. Requires the Bokeh library installed. """ from dna_features_viewer import BiopythonTranslator from bokeh.resources import CDN from bokeh.embed import file_html record = BiopythonTranslator().translate_record(record="example_sequence.gb") plot = record.plot_with_bokeh(figure_width=8) with open("plot_with_bokeh.html", "w+") as f: f.write(file_html(plot, CDN, "Example Sequence"))