def test_plot_multiple(tmpdir, basictrees, with_ete3):
plot = Plot(dummy=not with_ete3,
output=str(tmpdir.join('test')),
height=600,
width=800,
multiple=True)
list(plot.consume(basictrees))
def test_plot_annotated(tmpdir, basictrees, with_ete3):
annotated_trees = build_pipeline(
"annotate --f tests/argfiles/annotation.csv -k taxon",
source=basictrees)
plot = Plot(output=str(tmpdir.join('test')),
attribute="f1",
dummy=not with_ete3)
list(plot.consume(annotated_trees))
def test_plot(dummy=False):
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
with tempfile.NamedTemporaryFile() as fp:
plot = Plot(dummy=dummy, output=fp.name, height=600, width=800)
for x in plot.consume(trees):
pass
lines.close()
def test_plot_annotated(dummy=False):
lines = fileinput.input("tests/treefiles/basic.trees")
trees = NewickParser().consume(lines)
annotated_trees = build_pipeline(
"annotate --f tests/argfiles/annotation.csv -k taxon", source=trees)
with tempfile.NamedTemporaryFile() as fp:
plot = Plot(output=fp.name, attribute="f1", dummy=dummy)
for x in plot.consume(annotated_trees):
pass
lines.close()
def test_init_from_args(with_ete3):
if not with_ete3:
assert True
else:
Plot.init_from_args("")
def test_init_from_args(dummy=False):
if dummy:
assert True
else:
plot = Plot.init_from_args("")