def test_draw_overlay(self):
gene = genomic.Gene('12',
25357723,
25403870,
strand=STRAND.NEG,
name='KRAS')
marker = BioInterval('12', 25403865, name='splice site mutation')
t = build_transcript(cds_start=193,
cds_end=759,
exons=[(25403685, 25403865), (25398208, 25398329),
(25380168, 25380346), (25378548, 25378707),
(25357723, 25362845)],
gene=gene,
domains=[])
build_transcript(cds_start=198,
cds_end=425,
exons=[(25403685, 25403870), (25398208, 25398329),
(25362102, 25362845)],
gene=gene,
domains=[])
build_transcript(cds_start=65,
cds_end=634,
exons=[(25403685, 25403737), (25398208, 25398329),
(25380168, 25380346), (25378548, 25378707),
(25368371, 25368494), (25362365, 25362845)],
gene=gene,
domains=[
protein.Domain('domain1', [(1, 10)]),
protein.Domain('domain1', [(4, 10)])
],
is_best_transcript=True)
build_transcript(cds_start=65,
cds_end=634,
exons=[(25403698, 25403863), (25398208, 25398329),
(25386753, 25388160)],
gene=gene,
domains=[])
d = DiagramSettings()
for i, t in enumerate(gene.transcripts):
t.name = 'transcript {}'.format(i + 1)
scatterx = [x + 100 for x in range(gene.start, gene.end + 1, 400)]
scattery = [random.uniform(-0.2, 0.2) for x in scatterx]
s = ScatterPlot(list(zip(scatterx, scattery)),
'cna',
ymin=-1,
ymax=1,
yticks=[-1, 0, 1])
d.gene_min_buffer = 0
canvas = draw_multi_transcript_overlay(d,
gene,
vmarkers=[marker],
plots=[s, s])
self.assertEqual(2, len(canvas.elements)) # defs counts as element
if OUTPUT_SVG:
canvas.saveas('test_draw_overlay.svg')
def test_generate_gene_mapping_err(self):
# _generate_interval_mapping [genomic.IntergenicRegion(11:77361962_77361962+)] 1181.39453125 5 30 None 77356962 77366962)
ir = genomic.IntergenicRegion('11', 5000, 5000, STRAND.POS)
tgt_width = 1000
d = DiagramSettings()
d.gene_min_buffer = 10
# (self, canvas, gene, width, height, fill, label='', reference_genome=None)
draw_genes(d, self.canvas, [ir], tgt_width, [])
# _generate_interval_mapping ['Interval(29684391, 29684391)', 'Interval(29663998, 29696515)'] 1181.39453125 5 60 None 29662998 29697515
# def generate_interval_mapping(cls, input_intervals, target_width, ratio, min_width, buffer_length=None, start=None, end=None, min_inter_width=None)
itvls = [Interval(29684391, 29684391), Interval(29663998, 29696515)]
generate_interval_mapping(itvls, 1181.39, 5, 60, None, 29662998,
29697515)
def test_draw_consec_exons(self):
d = DiagramSettings()
# domains = [protein.Domain()]
t = build_transcript(
gene=None,
cds_start=50,
cds_end=249,
exons=[(1, 99), (200, 299), (300, 350), (400, 499)],
strand=STRAND.POS,
domains=[],
)
b = Breakpoint('1', 350, 410, orient=ORIENT.LEFT)
g = draw_ustranscript(d,
self.canvas,
t,
500,
colors={t.exons[1]: '#FFFF00'},
breakpoints=[b])
self.canvas.add(g)
if OUTPUT_SVG:
self.canvas.saveas('test_draw_consec_exons.svg')
# self.canvas.saveas('test_draw_ustranscript.svg')
self.assertEqual(2, len(self.canvas.elements))
self.assertEqual(3, len(g.elements))
# check that only 2 splicing marks were created
self.assertEqual(2, len(g.elements[0].elements[0].elements))
# get the second exon
ex2 = g.elements[0].elements[1].elements[2].elements[0]
print(ex2)
self.assertAlmostEqual(120.7783426339, ex2.attribs.get('width'))
# get the third exon
ex3 = g.elements[0].elements[1].elements[3].elements[0]
print(ex3)
self.assertAlmostEqual(96.52494419642852, ex3.attribs.get('width'))
def test_draw_consec_exons(self, canvas):
d = DiagramSettings(domain_name_regex_filter=r'.*')
# domains = [protein.Domain()]
t = build_transcript(
gene=None,
cds_start=50,
cds_end=249,
exons=[(1, 99), (200, 299), (300, 350), (400, 499)],
strand=STRAND.POS,
domains=[],
)
b = Breakpoint('1', 350, 410, orient=ORIENT.LEFT)
g = draw_ustranscript(d,
canvas,
t,
500,
colors={t.exons[1]: '#FFFF00'},
breakpoints=[b])
canvas.add(g)
if OUTPUT_SVG:
canvas.saveas('test_draw_consec_exons.svg')
# canvas.saveas('test_draw_ustranscript.svg')
assert len(canvas.elements) == 2
assert len(g.elements) == 3
# check that only 2 splicing marks were created
assert len(g.elements[0].elements[0].elements) == 2
# get the second exon
ex2 = g.elements[0].elements[1].elements[2].elements[0]
print(ex2)
assert pytest.approx(ex2.attribs.get('width')) == 120.7783426339
# get the third exon
ex3 = g.elements[0].elements[1].elements[3].elements[0]
print(ex3)
assert pytest.approx(ex3.attribs.get('width')) == 96.52494419642852
def test_single_bp_ins_exon(self):
transcript = fusion.FusionTranscript()
transcript.position = Interval(401258, 408265)
transcript.exons = [
genomic.Exon(401258, 401461, transcript=transcript),
genomic.Exon(404799,
405254,
intact_end_splice=False,
transcript=transcript),
genomic.Exon(
405255,
405255,
intact_start_splice=False,
intact_end_splice=False,
transcript=transcript,
),
genomic.Exon(405256,
408265,
intact_start_splice=False,
transcript=transcript),
]
cfg = DiagramSettings(width=1500)
canvas = Drawing(size=(cfg.width, 1000))
drawing_width = cfg.width - cfg.label_left_margin - cfg.left_margin - cfg.right_margin
canvas.add(
draw_ustranscript(cfg,
canvas,
transcript,
target_width=drawing_width))
if OUTPUT_SVG:
canvas.saveas('test_single_bp_ins_exon.svg')
def test_single_bp_dup(self):
transcript = fusion.FusionTranscript()
transcript.position = Interval(1, 500)
transcript.exons = [
genomic.Exon(1, 7, transcript=transcript, intact_end_splice=False),
genomic.Exon(8,
8,
transcript=transcript,
intact_start_splice=False,
intact_end_splice=False),
genomic.Exon(9,
100,
transcript=transcript,
intact_start_splice=False),
genomic.Exon(200, 500, transcript=transcript),
]
cfg = DiagramSettings(width=1500)
canvas = Drawing(size=(cfg.width, 1000))
drawing_width = cfg.width - cfg.label_left_margin - cfg.left_margin - cfg.right_margin
canvas.add(
draw_ustranscript(cfg,
canvas,
transcript,
target_width=drawing_width))
if OUTPUT_SVG:
canvas.saveas('test_single_bp_dup.svg')
def test_draw_template(self):
# def draw_template(self, canvas, template, target_width, height, labels=None, colors=None):
d = DiagramSettings()
canvas = Drawing(size=(1000, 50))
t = genomic.Template(
'1',
1,
100000,
bands=[
BioInterval(None, 1, 8000, 'p1'),
BioInterval(None, 10000, 15000, 'p2')
],
)
g = draw_template(d, canvas, t, 1000)
canvas.add(g)
canvas.attribs['height'] = g.height
canvas = Drawing(size=(1000, 50))
g = draw_template(d, canvas, TEMPLATE_METADATA['1'], 1000)
self.assertEqual(
d.breakpoint_top_margin + d.breakpoint_bottom_margin +
d.template_track_height, g.height)
canvas.add(g)
canvas.attribs['height'] = g.height
self.assertEqual(2, len(canvas.elements))
def test_draw_genes(self):
x = genomic.Gene('1', 1000, 2000, strand=STRAND.POS)
y = genomic.Gene('1', 5000, 7000, strand=STRAND.NEG)
z = genomic.Gene('1', 1500, 2500, strand=STRAND.POS)
d = DiagramSettings()
breakpoints = [Breakpoint('1', 1100, 1200, orient=ORIENT.RIGHT)]
g = draw_genes(d, self.canvas, [x, y, z], 500, breakpoints, {
x: d.gene1_color,
y: d.gene2_color_selected,
z: d.gene2_color
})
# test the class structure
self.assertEqual(6, len(g.elements))
self.assertEqual('scaffold', g.elements[0].attribs.get('class', ''))
for i in range(1, 4):
self.assertEqual('gene', g.elements[i].attribs.get('class', ''))
self.assertEqual('mask', g.elements[4].attribs.get('class', ''))
self.assertEqual('breakpoint', g.elements[5].attribs.get('class', ''))
self.assertEqual(
d.track_height * 2 + d.padding + d.breakpoint_bottom_margin +
d.breakpoint_top_margin, g.height)
self.canvas.add(g)
self.assertEqual(len(g.labels), 4)
self.assertEqual(x, g.labels['G1'])
self.assertEqual(z, g.labels['G2'])
self.assertEqual(y, g.labels['G3'])
self.assertEqual(breakpoints[0], g.labels['B1'])
def test_draw_layout_single_genomic(self):
d = DiagramSettings()
d1 = protein.Domain('first', [(55, 61), (71, 73)])
d2 = protein.Domain('second', [(10, 20), (30, 34)])
g1 = genomic.Gene('1', 150, 1000, strand=STRAND.POS)
g2 = genomic.Gene('1', 5000, 7500, strand=STRAND.POS)
t1 = build_transcript(
gene=g1,
cds_start=50,
cds_end=249,
exons=[(200, 299), (400, 499), (700, 899)],
domains=[d2, d1],
)
t2 = build_transcript(
gene=g2,
cds_start=20,
cds_end=500,
exons=[(5100, 5299), (5800, 6199), (6500, 6549), (6700, 6799)],
domains=[],
)
b1 = Breakpoint('1', 350, orient=ORIENT.LEFT)
b2 = Breakpoint('1', 6500, orient=ORIENT.RIGHT)
bpp = BreakpointPair(b1,
b2,
opposing_strands=False,
untemplated_seq='')
ann = variant.Annotation(bpp,
transcript1=t1,
transcript2=t2,
event_type=SVTYPE.DEL,
protocol=PROTOCOL.GENOME)
ann.add_gene(genomic.Gene('1', 1500, 1950, strand=STRAND.POS))
ann.add_gene(genomic.Gene('1', 3000, 3980, strand=STRAND.POS))
ann.add_gene(genomic.Gene('1', 3700, 4400, strand=STRAND.NEG))
reference_genome = {'1': MockObject(seq=MockString('A'))}
ft = variant.FusionTranscript.build(ann, reference_genome)
ann.fusion = ft
self.assertEqual(t1.exons[0], ft.exon_mapping[ft.exons[0].position])
self.assertEqual(t2.exons[2], ft.exon_mapping[ft.exons[1].position])
self.assertEqual(t2.exons[3], ft.exon_mapping[ft.exons[2].position])
canvas, legend = draw_sv_summary_diagram(d, ann)
self.assertEqual(5, len(canvas.elements)) # defs counts as element
expected_height = (d.top_margin + d.bottom_margin + d.track_height +
d.breakpoint_bottom_margin +
d.breakpoint_top_margin + d.inner_margin +
d.track_height + d.splice_height +
d.breakpoint_bottom_margin +
d.breakpoint_top_margin + d.padding +
d.translation_track_height + d.padding * 2 +
d.domain_track_height * 2 + d.inner_margin +
d.track_height + d.splice_height)
self.assertEqual(expected_height, canvas.attribs['height'])
if OUTPUT_SVG:
canvas.saveas('test_draw_layout_single_genomic.svg')
def test_draw_layout_translocation(self):
d = DiagramSettings(domain_name_regex_filter=r'.*')
d1 = protein.Domain('first', [(55, 61), (71, 73)])
d2 = protein.Domain('second', [(10, 20), (30, 34)])
g1 = genomic.Gene('1', 150, 1000, strand=STRAND.POS)
g2 = genomic.Gene('2', 5000, 7500, strand=STRAND.NEG)
t1 = build_transcript(
gene=g1,
cds_start=50,
cds_end=249,
exons=[(200, 299), (400, 499), (700, 899)],
domains=[d2, d1],
)
t2 = build_transcript(
gene=g2,
cds_start=120,
cds_end=700,
exons=[(5100, 5299), (5800, 6199), (6500, 6549), (6700, 6799)],
domains=[],
)
b1 = Breakpoint('1', 350, orient=ORIENT.LEFT)
b2 = Breakpoint('2', 6520, orient=ORIENT.LEFT)
bpp = BreakpointPair(b1, b2, opposing_strands=True, untemplated_seq='')
ann = variant.Annotation(bpp,
transcript1=t1,
transcript2=t2,
event_type=SVTYPE.ITRANS,
protocol=PROTOCOL.GENOME)
# genes 1
ann.add_gene(genomic.Gene('1', 1500, 1950, strand=STRAND.POS))
ann.add_gene(genomic.Gene('1', 3000, 3980, strand=STRAND.POS))
ann.add_gene(genomic.Gene('1', 3700, 4400, strand=STRAND.NEG))
# genes 2
ann.add_gene(genomic.Gene('2', 1500, 1950, strand=STRAND.NEG))
ann.add_gene(genomic.Gene('2', 5500, 9000, strand=STRAND.POS))
ann.add_gene(genomic.Gene('2', 3700, 4400, strand=STRAND.NEG))
reference_genome = {
'1': MockObject(seq=MockString('A')),
'2': MockObject(seq=MockString('A')),
}
ft = variant.FusionTranscript.build(ann, reference_genome)
ann.fusion = ft
canvas, legend = draw_sv_summary_diagram(d, ann)
assert len(canvas.elements) == 6 # defs counts as element
expected_height = (
d.top_margin + d.bottom_margin + d.track_height * 2 + d.padding +
d.breakpoint_bottom_margin + d.breakpoint_top_margin +
d.inner_margin + d.track_height + d.splice_height +
d.breakpoint_bottom_margin + d.breakpoint_top_margin + d.padding +
d.translation_track_height + d.padding * 2 +
d.domain_track_height * 2 + d.inner_margin + d.track_height +
d.splice_height)
assert canvas.attribs['height'] == expected_height
def test_draw_ustranscript(self):
d = DiagramSettings()
# domains = [protein.Domain()]
d1 = protein.Domain('first', [(55, 61), (71, 73)])
d2 = protein.Domain('second', [(10, 20), (30, 34)])
t = build_transcript(
gene=None,
cds_start=50,
cds_end=249,
exons=[(1, 99), (200, 299), (400, 499)],
strand=STRAND.NEG,
domains=[d2, d1],
)
b = Breakpoint('1', 350, 410, orient=ORIENT.LEFT)
g = draw_ustranscript(d,
self.canvas,
t,
500,
colors={t.exons[1]: '#FFFF00'},
breakpoints=[b])
self.canvas.add(g)
# self.canvas.saveas('test_draw_ustranscript.svg')
self.assertEqual(2, len(self.canvas.elements))
self.assertEqual(3, len(g.elements))
for el, cls in zip(g.elements[0].elements,
['splicing', 'exon_track', 'protein']):
self.assertEqual(cls, el.attribs.get('class', ''))
for el, cls in zip(g.elements[0].elements[1].elements,
['scaffold', 'exon', 'exon', 'exon']):
self.assertEqual(cls, el.attribs.get('class', ''))
for el, cls in zip(g.elements[0].elements[2].elements,
['translation', 'domain', 'domain']):
self.assertEqual(cls, el.attribs.get('class', ''))
self.assertEqual(
sum([
d.track_height,
d.splice_height,
2 * d.padding,
d.domain_track_height * 2,
d.translation_track_height,
d.padding,
d.breakpoint_top_margin,
d.breakpoint_bottom_margin,
]),
g.height,
)
self.assertEqual(d1.name, g.labels['D1'])
self.assertEqual(d2.name, g.labels['D2'])
def test_draw_legend(self):
d = DiagramSettings()
swatches = [('#000000', 'black'), ('#FF0000', 'red'),
('#0000FF', 'blue'), ('#00FF00', 'green'),
('#FFFF00', 'yellow')]
g = draw_legend(d, self.canvas, swatches)
self.canvas.add(g)
self.assertEqual('legend', g.attribs.get('class', ''))
self.assertEqual(
d.legend_swatch_size * len(swatches) + d.padding *
(len(swatches) - 1 + 2), g.height)
self.assertEqual(6, len(g.elements))
self.assertEqual(
6 * d.legend_font_size * d.font_width_height_ratio +
d.padding * 3 + d.legend_swatch_size, g.width)
def test_two_exon_transcript(self):
transcript = fusion.FusionTranscript()
transcript.position = Interval(1, 555)
transcript.exons = [
genomic.Exon(55820038, 55820969, transcript=transcript),
genomic.Exon(55820971, 55820976, transcript=transcript),
]
transcript.exon_mapping[Interval(55820971, 55820976)] = MockObject(
transcript=MockObject(exon_number=lambda *x: 2))
cfg = DiagramSettings(width=1500)
canvas = Drawing(size=(cfg.width, 1000))
drawing_width = cfg.width - cfg.label_left_margin - cfg.left_margin - cfg.right_margin
canvas.add(
draw_ustranscript(cfg,
canvas,
transcript,
target_width=drawing_width))
if OUTPUT_SVG:
canvas.saveas('test_two_exon_transcript.svg')
def test_draw_legend(self, canvas):
d = DiagramSettings(domain_name_regex_filter=r'.*')
swatches = [
('#000000', 'black'),
('#FF0000', 'red'),
('#0000FF', 'blue'),
('#00FF00', 'green'),
('#FFFF00', 'yellow'),
]
g = draw_legend(d, canvas, swatches)
canvas.add(g)
assert g.attribs.get('class', '') == 'legend'
assert g.height == d.legend_swatch_size * len(swatches) + d.padding * (
len(swatches) - 1 + 2)
assert len(g.elements) == 6
assert (g.width == 6 * d.legend_font_size * d.font_width_height_ratio +
d.padding * 3 + d.legend_swatch_size)
def test_draw_layout_single_transcript(self):
d = DiagramSettings()
d1 = protein.Domain('first', [(55, 61), (71, 73)])
d2 = protein.Domain('second', [(10, 20), (30, 34)])
g1 = genomic.Gene('1', 150, 1000, strand=STRAND.POS)
t = build_transcript(g1, [(200, 299), (400, 499), (700, 899)], 50, 249,
[d2, d1])
b1 = Breakpoint('1', 350, orient=ORIENT.RIGHT)
b2 = Breakpoint('1', 600, orient=ORIENT.LEFT)
bpp = BreakpointPair(b1,
b2,
opposing_strands=False,
untemplated_seq='')
ann = variant.Annotation(bpp,
transcript1=t,
transcript2=t,
event_type=SVTYPE.DUP,
protocol=PROTOCOL.GENOME)
ann.add_gene(genomic.Gene('1', 1500, 1950, strand=STRAND.POS))
reference_genome = {'1': MockObject(seq=MockString('A'))}
ft = variant.FusionTranscript.build(ann, reference_genome)
ann.fusion = ft
canvas, legend = draw_sv_summary_diagram(d, ann)
self.assertEqual(4, len(canvas.elements)) # defs counts as element
expected_height = (d.top_margin + d.bottom_margin + d.track_height +
d.breakpoint_bottom_margin +
d.breakpoint_top_margin + d.inner_margin +
d.track_height + d.splice_height + d.padding +
d.translation_track_height + d.padding * 2 +
d.domain_track_height * 2 + d.inner_margin +
d.track_height + d.breakpoint_bottom_margin +
d.breakpoint_top_margin + d.splice_height)
if OUTPUT_SVG:
canvas.saveas('test_draw_layout_single_transcript.svg')
self.assertEqual(expected_height, canvas.attribs['height'])
def test_draw_genes(self, canvas):
x = genomic.Gene('1', 1000, 2000, strand=STRAND.POS)
y = genomic.Gene('1', 5000, 7000, strand=STRAND.NEG)
z = genomic.Gene('1', 1500, 2500, strand=STRAND.POS)
d = DiagramSettings(domain_name_regex_filter=r'.*')
breakpoints = [Breakpoint('1', 1100, 1200, orient=ORIENT.RIGHT)]
g = draw_genes(
d,
canvas,
[x, y, z],
500,
breakpoints,
{
x: d.gene1_color,
y: d.gene2_color_selected,
z: d.gene2_color
},
)
# test the class structure
assert len(g.elements) == 6
assert g.elements[0].attribs.get('class', '') == 'scaffold'
for i in range(1, 4):
assert g.elements[i].attribs.get('class', '') == 'gene'
assert g.elements[4].attribs.get('class', '') == 'mask'
assert g.elements[5].attribs.get('class', '') == 'breakpoint'
assert (g.height == d.track_height * 2 + d.padding +
d.breakpoint_bottom_margin + d.breakpoint_top_margin)
canvas.add(g)
assert 4 == len(g.labels)
assert g.labels['G1'] == x
assert g.labels['G2'] == z
assert g.labels['G3'] == y
assert g.labels['B1'] == breakpoints[0]
def test_draw_translocation_with_template(self):
d = DiagramSettings()
d1 = protein.Domain('PF0001', [(55, 61), (71, 73)])
d2 = protein.Domain('PF0002', [(10, 20), (30, 34)])
g1 = genomic.Gene(TEMPLATE_METADATA['1'],
150,
1000,
strand=STRAND.POS,
aliases=['HUGO2'])
g2 = genomic.Gene(TEMPLATE_METADATA['X'],
5000,
7500,
strand=STRAND.NEG,
aliases=['HUGO3'])
t1 = build_transcript(
gene=g1,
name='transcript1',
cds_start=50,
cds_end=249,
exons=[(200, 299), (400, 499), (700, 899)],
domains=[d2, d1],
)
t2 = build_transcript(
gene=g2,
name='transcript2',
cds_start=120,
cds_end=700,
exons=[(5100, 5299), (5800, 6199), (6500, 6549), (6700, 6799)],
domains=[],
)
b1 = Breakpoint('1', 350, orient=ORIENT.LEFT)
b2 = Breakpoint('2', 6520, orient=ORIENT.LEFT)
bpp = BreakpointPair(b1, b2, opposing_strands=True, untemplated_seq='')
ann = variant.Annotation(bpp,
transcript1=t1,
transcript2=t2,
event_type=SVTYPE.ITRANS,
protocol=PROTOCOL.GENOME)
# genes 1
ann.add_gene(
genomic.Gene('1', 1500, 1950, strand=STRAND.POS,
aliases=['HUGO5']))
ann.add_gene(genomic.Gene('1', 3000, 3980, strand=STRAND.POS))
ann.add_gene(genomic.Gene('1', 3700, 4400, strand=STRAND.NEG))
# genes 2
ann.add_gene(genomic.Gene('2', 1500, 1950, strand=STRAND.NEG))
ann.add_gene(genomic.Gene('2', 5500, 9000, strand=STRAND.POS))
ann.add_gene(genomic.Gene('2', 3700, 4400, strand=STRAND.NEG))
reference_genome = {
'1': MockObject(seq=MockString('A')),
'2': MockObject(seq=MockString('A')),
}
ft = variant.FusionTranscript.build(ann, reference_genome)
ann.fusion = ft
canvas, legend = draw_sv_summary_diagram(d,
ann,
draw_reference_templates=True,
templates=TEMPLATE_METADATA)
if OUTPUT_SVG:
canvas.saveas('test_draw_translocation_with_template.svg')
self.assertEqual(8, len(canvas.elements)) # defs counts as element
expected_height = (
d.top_margin + d.bottom_margin + d.track_height * 2 + d.padding +
d.breakpoint_bottom_margin + d.breakpoint_top_margin +
d.inner_margin + d.track_height + d.splice_height +
d.breakpoint_bottom_margin + d.breakpoint_top_margin + d.padding +
d.translation_track_height + d.padding * 2 +
d.domain_track_height * 2 + d.inner_margin * 2 + d.track_height +
d.breakpoint_bottom_margin + d.breakpoint_top_margin +
d.splice_height + d.template_track_height)
self.assertAlmostEqual(expected_height, canvas.attribs['height'])
