def test_summarize_zero_coverage():
figure = Figure()
figure.add(Coverage(10, 20, [0, 0, 0]), gap=-4)
figure.add(Track(10, 20, label="Bar"))
with pytest.raises(ZeroDivisionError):
summarize_figure(figure)
def test_summarize_smooth_coverage():
figure = Figure()
figure.add(SmoothCoverage(10, 20, [11, 11, 21, 1, 1, 1]), gap=-4)
figure.add(Track(12, 22, label="Bar"))
expected_summary = """\
Coverage 11x2, 21, 1x3
Bar[12-22]
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_arrow():
figure = Figure()
figure.add(Arrow(10, 50, label='Foo'))
figure.add(Arrow(60, 30, label='Bar'))
expected_summary = """\
10--Foo->50
30<-Bar--60
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_label_objects():
figure = Figure()
figure.add(Track(0, 0, label=Label(25, "Foo:")))
figure.add(Track(0, 0, label="Bar:"))
expected_summary = """\
Foo:
Bar:
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_smooth_coverage_ten_percent():
figure = Figure()
figure.add(SmoothCoverage(10, 20, [100, 110, 111, 50]), gap=-4)
figure.add(Track(12, 22, label="Bar"))
expected_summary = """\
Coverage 100x2, 111, 50
Bar[12-22]
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_labels():
figure = Figure()
figure.add(Track(1, 200, label="Foo"))
figure.add(Track(1, 200, label="Bar", color='none'))
expected_summary = """\
Foo[1-200]
Bar(1-200)
"""
summary = summarize_figure(figure)
assert summary == expected_summary
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_summarize_regions():
figure = Figure()
figure.add(
Track(1,
200,
label="Foo",
regions=[(50, 100, 'lightgreen'), (110, 120, 'red')]))
expected_summary = """\
Foo[1-200], lightgreen{50-100}, red{110-120}
"""
summary = summarize_figure(figure)
assert summary == expected_summary
def test_summarize_multitracks():
figure = Figure()
figure.add(Track(0, 0, label="Foo:"))
figure.add(
Multitrack([Track(10, 20, label="Bar"),
Track(30, 40, label="Baz")]))
expected_summary = """\
Foo:
Bar[10-20], Baz[30-40]
"""
summary = summarize_figure(figure)
assert summary == expected_summary
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')
def test_summarize_arrow_group():
figure = Figure()
figure.add(
ArrowGroup([Arrow(10, 50, label='Foo'),
Arrow(60, 30, label='Bar')]))
figure.add(
ArrowGroup([Arrow(1, 50, label='Baz'),
Arrow(90, 100, label='Boom')]))
expected_summary = """\
10--Foo->50, 30<-Bar--60
1--Baz->50, 90--Boom->100
"""
summary = summarize_figure(figure)
assert summary == expected_summary
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_summarize_multitracks_with_separate_label():
figure = Figure()
figure.add(Track(0, 0, label="Foo:"))
figure.add(
Multitrack([
Track(10, 20),
Track(30, 40),
Track(10, 40, label="Bar", color='none')
]))
expected_summary = """\
Foo:
[10-20], [30-40], Bar(10-40)
"""
summary = summarize_figure(figure)
assert summary == expected_summary
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 start_drawing(width, height):
expected_svg = Drawing(width, height, origin=(0, 0))
expected_svg.append(
Rectangle(0,
height - 15,
200,
10,
stroke='lightgrey',
fill='lightgrey'))
expected_svg.append(
Text('Header',
10,
width / 2,
height - 15,
font_family='monospace',
text_anchor='middle'))
f = Figure()
f.add(Track(0, width, label='Header'))
return f, expected_svg
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 build_coverage_figure(genome_coverage_csv, blast_csv=None):
min_position, max_position = 1, 500
coordinate_depths = Counter()
contig_depths = Counter()
contig_groups = defaultdict(set) # {coordinates_name: {contig_name}}
reader = DictReader(genome_coverage_csv)
for row in reader:
query_nuc_pos = int(row['query_nuc_pos'])
if row['refseq_nuc_pos']:
refseq_nuc_pos = int(row['refseq_nuc_pos'])
else:
refseq_nuc_pos = min_position
min_position = min(min_position, refseq_nuc_pos, query_nuc_pos)
max_position = max(max_position, refseq_nuc_pos, query_nuc_pos)
coordinates_name = row['coordinates']
contig_name = row['contig']
if row['coverage'] != '':
row_coverage = int(row['coverage']) - int(row['dels'])
coordinate_depths[coordinates_name] = max(
coordinate_depths[coordinates_name], row_coverage)
contig_depths[contig_name] = max(contig_depths[contig_name],
row_coverage)
contig_groups[coordinates_name].add(contig_name)
if '' in coordinate_depths:
# Force partial contigs to come last.
coordinate_depths[''] = -1
position_offset = -min_position + 1
max_position += position_offset
blast_rows = []
if blast_csv is not None:
for blast_row in DictReader(blast_csv):
for field_name in ('start', 'end', 'ref_start', 'ref_end'):
# noinspection PyTypeChecker
blast_row[field_name] = int(blast_row[field_name])
blast_rows.append(blast_row)
blast_rows.sort(key=itemgetter('start', 'ref_start'))
landmarks_path = (Path(__file__).parent.parent / "data" /
"landmark_references.yaml")
landmark_groups = yaml.safe_load(landmarks_path.read_text())
projects = ProjectConfig.loadDefault()
f = Figure()
for _, coordinates_name in sorted(
(-depth, name) for name, depth in coordinate_depths.items()):
for reference_set in landmark_groups:
if coordinates_name != reference_set['coordinates']:
continue
prev_landmark = None
for i, landmark in enumerate(
sorted(reference_set['landmarks'],
key=itemgetter('start'))):
landmark.setdefault('frame', 0)
if prev_landmark and 'end' not in prev_landmark:
prev_landmark['end'] = landmark['start'] - 1
prev_landmark = landmark
for frame, frame_landmarks in groupby(reference_set['landmarks'],
itemgetter('frame')):
subtracks = []
for landmark in frame_landmarks:
landmark_colour = landmark.get('colour')
if landmark_colour is None:
continue
subtracks.append(
Track(landmark['start'] + position_offset,
landmark['end'] + position_offset,
label=landmark['name'],
color=landmark_colour))
max_position = max(max_position,
landmark['end'] + position_offset)
f.add(Multitrack(subtracks))
break
else:
add_partial_banner(f, position_offset, max_position)
contig_names = contig_groups[coordinates_name]
sorted_contig_names = sort_contig_names(contig_names, contig_depths)
ref_arrows = []
for contig_name in sorted_contig_names:
if contig_name.startswith('contig-'):
# No arrows on original contig tracks.
continue
contig_matcher = ContigMatcher(contig_name)
ref_positions = None
arrow_count = 0
for blast_row in blast_rows:
if not contig_matcher.is_match(blast_row):
continue
if (ref_positions is None and coordinates_name != ''
and blast_row['ref_name'] != coordinates_name):
ref_positions = map_references(blast_row['ref_name'],
coordinates_name, projects)
arrow_count += 1
ref_start = int(blast_row['ref_start'])
ref_end = int(blast_row['ref_end'])
if ref_positions is None:
coordinate_start = ref_start
coordinate_end = ref_end
else:
coordinate_start = ref_positions[ref_start]
coordinate_end = ref_positions[ref_end]
ref_arrows.append(
Arrow(coordinate_start + position_offset,
coordinate_end + position_offset,
elevation=1,
label=f'{contig_matcher.num}.{arrow_count}'))
if ref_arrows:
f.add(ArrowGroup(ref_arrows))
for contig_name in sorted_contig_names:
genome_coverage_csv.seek(0)
reader = DictReader(genome_coverage_csv)
build_contig(reader, f, contig_name, max_position, position_offset,
blast_rows)
if not f.elements:
f.add(Track(1, max_position, label='No contigs found.', color='none'))
return f