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_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_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_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_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')
