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"))
