def test_add_track(self):
figure = Figure()
figure.add_track(
Track(50,
300,
direction='f',
label="Another\
sequence",
regions=[(50, 100, 'lightblue')]))
figure.add_track(Track(110, 410, direction='r', label="Sequence 1",\
regions=[(150, 200, 'salmon')]))
figure.show()
def summarize_figure(figure: Figure):
""" Summarize the contents of a figure to text.
Useful for testing.
"""
figure.show() # Test that all the display math works.
summary = StringIO()
for padding, track in figure.elements:
spans = getattr(track, 'arrows', None)
if spans is None:
spans = getattr(track, 'tracks', [track])
else:
spans.sort(key=attrgetter('x', 'w', 'label'))
for i, span in enumerate(spans):
if i:
summary.write(', ')
ys = getattr(span, 'ys', None)
if ys is not None:
summary.write('Coverage ')
summary.write(', '.join(map(str, ys)))
continue
coverage_groups = getattr(span, 'coverage_groups', None)
if coverage_groups is not None:
summary.write('Coverage ')
for j, (y, count) in enumerate(coverage_groups):
if j:
summary.write(', ')
summary.write(str(y))
if count > 1:
summary.write(f'x{count}')
continue
direction = getattr(span, 'direction', None)
if direction is not None and direction != '':
if direction >= 0:
summary.write(f'{span.x}--{span.label}->{span.x+span.w}')
else:
summary.write(f'{span.x}<-{span.label}--{span.x+span.w}')
continue
span_text = getattr(span.label, 'text', span.label) or ''
summary.write(span_text)
color = getattr(span, 'color')
if span.a or span.b:
if color != 'none':
summary.write(f'[{span.a}-{span.b}]')
else:
summary.write(f'({span.a}-{span.b})')
regions = getattr(span, 'regions', [])
for start, end, colour in regions:
summary.write(f', {colour}{{{start}-{end}}}')
summary.write('\n')
return summary.getvalue()
def test_multitrack(self):
figure = Figure()
for i in range(0, 10):
figure.add_track(
Multitrack([
Track(
i, i + 10, direction='f', label='Track {}F'.format(i)),
Track(i + 20,
i + 30,
direction='r',
label='Track {}R'.format(i))
],
join=True))
figure.show()
def test_draw_coverage(svg_differ):
expected_figure = Figure()
expected_figure.add(Track(0, 1, color='', h=-4)) # Just a spacer.
expected_figure.add(Track(100, 200, label='Bar'))
expected_svg = expected_figure.show()
expected_svg.insert(0, draw.Rectangle(100, 20, 25, 5, fill='blue'))
expected_svg.insert(1, draw.Rectangle(125, 20, 25, 10, fill='blue'))
expected_svg.insert(2, draw.Rectangle(175, 20, 25, 1, fill='blue'))
figure = Figure()
coverage_depths = 25 * [5] + 25 * [10] + 25 * [0] + 25 * [1]
figure.add(SmoothCoverage(100, 200, coverage_depths), gap=-4)
figure.add(Track(100, 200, label="Bar"))
svg = figure.show()
svg_differ.assert_equal(svg, expected_svg, 'test_draw_coverage')
def test_arrow_group_reverse_overlap(svg_differ):
expected_figure = Figure()
expected_figure.add(Track(1, 500, label='Header'))
h = 20
expected_figure.add(Arrow(1, 300, label='X', h=h), gap=3)
expected_figure.add(Arrow(400, 250, label='Y', h=h))
expected_svg = expected_figure.show()
f = Figure()
f.add(Track(1, 500, label='Header'))
f.add(
ArrowGroup(
[Arrow(1, 300, label='X', h=h),
Arrow(400, 250, label='Y', h=h)]))
svg = f.show()
svg_differ.assert_equal(svg, expected_svg, 'test_arrow_group')
def test_arrow_group(svg_differ):
expected_figure = Figure()
expected_figure.add(Track(1, 500, label='Header'))
h = 30
expected_figure.add(Arrow(1, 200, label='X', h=h), gap=-h)
expected_figure.add(Arrow(300, 500, label='Y', h=h))
expected_svg = expected_figure.show()
f = Figure()
f.add(Track(1, 500, label='Header'))
f.add(
ArrowGroup(
[Arrow(1, 200, label='X', h=h),
Arrow(300, 500, label='Y', h=h)]))
svg = f.show()
svg_differ.assert_equal(svg, expected_svg, 'test_arrow_group')
def test_arrow_group_small_neighbour(svg_differ):
expected_figure = Figure()
expected_figure.add(Track(1, 500, label='Header'))
h = 20
expected_figure.add(Arrow(301, 315, elevation=-1, label='1.2', h=h),
gap=-h)
expected_figure.add(Arrow(1, 300, elevation=-1, label='1.1', h=h))
expected_svg = expected_figure.show()
f = Figure()
f.add(Track(1, 500, label='Header'))
f.add(
ArrowGroup([
Arrow(1, 300, elevation=-1, label='1.1', h=h),
Arrow(301, 315, elevation=-1, label='1.2', h=h)
]))
svg = f.show()
svg_differ.assert_equal(svg, expected_svg, 'test_arrow_group')
def test_tiny_arrow_at_edge(svg_differ):
expected_svg = Drawing(210, 35, origin=(0, 0))
expected_svg.append(Circle(197.5, 20, 10, stroke='black', fill='ivory'))
expected_svg.append(
Text('2.3', 11, 197.5, 20, text_anchor='middle', dy="0.35em"))
expected_svg.append(
Lines(200, 10, 195, 13.5, 195, 6.5, 200, 10, fill='black'))
f = Figure()
f.add(ArrowGroup([Arrow(195, 200, h=20, elevation=-1, label='2.3')]))
svg = f.show()
svg_differ.assert_equal(svg, expected_svg, 'test_arrow')
def test_scaled_arrow(svg_differ):
expected_svg = Drawing(100, 35, origin=(0, 0))
expected_svg.append(Line(0, 10, 93, 10, stroke='black'))
expected_svg.append(Circle(50, 20, 10, stroke='black', fill='ivory'))
expected_svg.append(
Text('2.3', 11, 50, 20, text_anchor='middle', dy="0.35em"))
expected_svg.append(
Lines(100, 10, 93, 13.5, 93, 6.5, 100, 10, fill='black'))
f = Figure()
f.add(Arrow(0, 200, h=20, elevation=-1, label='2.3'))
svg = f.show(w=100)
svg_differ.assert_equal(svg, expected_svg, 'test_arrow')