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_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'])