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_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_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_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_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'])