def test_deletion_or_insertion(self):
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.POS, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.POS, orient=ORIENT.RIGHT))
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(b)))
b = BreakpointPair(Breakpoint(1,
1,
2,
strand=STRAND.POS,
orient=ORIENT.LEFT),
Breakpoint(1,
10,
11,
strand=STRAND.NS,
orient=ORIENT.RIGHT),
opposing_strands=False)
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(b)))
b = BreakpointPair(
Breakpoint(1, 1, 2, strand=STRAND.NEG, orient=ORIENT.LEFT),
Breakpoint(1, 10, 11, strand=STRAND.NEG, orient=ORIENT.RIGHT))
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(b)))
b = BreakpointPair(Breakpoint(1,
1,
2,
strand=STRAND.NEG,
orient=ORIENT.LEFT),
Breakpoint(1,
10,
11,
strand=STRAND.NS,
orient=ORIENT.RIGHT),
opposing_strands=False)
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(b)))
b = BreakpointPair(Breakpoint(1,
1,
2,
strand=STRAND.NS,
orient=ORIENT.LEFT),
Breakpoint(1,
10,
11,
strand=STRAND.POS,
orient=ORIENT.RIGHT),
opposing_strands=False)
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(b)))
b = BreakpointPair(Breakpoint(1,
1,
2,
strand=STRAND.NS,
orient=ORIENT.LEFT),
Breakpoint(1,
10,
11,
strand=STRAND.NEG,
orient=ORIENT.RIGHT),
opposing_strands=False)
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(b)))
b = BreakpointPair(Breakpoint(1,
1,
2,
strand=STRAND.NS,
orient=ORIENT.LEFT),
Breakpoint(1,
10,
11,
strand=STRAND.NS,
orient=ORIENT.RIGHT),
opposing_strands=False)
self.assertEqual(sorted([SVTYPE.DEL, SVTYPE.INS]),
sorted(BreakpointPair.classify(b)))
def test_deletion_no_distance_error(self):
bpp = BreakpointPair(Breakpoint('1', 7039, orient='L'),
Breakpoint('1', 7040, orient='R'),
opposing=False)
self.assertEqual(sorted([SVTYPE.INS]),
sorted(BreakpointPair.classify(bpp)))
def test_inverted_translocation(self):
b = BreakpointPair(Breakpoint(1, 1, 2, ORIENT.LEFT),
Breakpoint(2, 1, 2, ORIENT.LEFT),
opposing_strands=True)
BreakpointPair.classify(b)
def test_translocation(self):
b = BreakpointPair(Breakpoint(1, 1, 2, ORIENT.RIGHT),
Breakpoint(2, 1, 2, ORIENT.LEFT),
opposing_strands=False)
BreakpointPair.classify(b)
def test___init__stranded(self):
with self.assertRaises(NotSpecifiedError):
BreakpointPair(Breakpoint('1', 1),
Breakpoint('1', 2),
stranded=True,
opposing_strands=True)
def test___init__invalid_inter_lr_opp(self):
with self.assertRaises(InvalidRearrangement):
BreakpointPair(Breakpoint(1, 1, 2, ORIENT.LEFT),
Breakpoint(2, 1, 2, ORIENT.RIGHT),
opposing_strands=True)
def test___init__opstrand_not_specified(self):
with self.assertRaises(NotSpecifiedError):
BreakpointPair(Breakpoint('1', 1), Breakpoint('1', 2))
def test___init__opstrand_conflict(self):
with self.assertRaises(AssertionError):
BreakpointPair(Breakpoint('1', 1, strand=STRAND.POS),
Breakpoint('1', 2, strand=STRAND.POS),
opposing_strands=True)
def test_insertion_in_intron(self):
# 55238868_55238906
bpp = BreakpointPair(Breakpoint('7', 5523750, orient=ORIENT.LEFT),
Breakpoint('7', 5523751, orient=ORIENT.RIGHT),
untemplated_seq='TTATCG')
self.assertEqual(Interval(6), bpp.net_size(self.egfr_distance))
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'])
def test___init__opstrand_indv_not_specified(self):
bpp = BreakpointPair(Breakpoint('test', 1), Breakpoint('test', 10), opposing_strands=True)
self.assertTrue(bpp.opposing_strands)
bpp = BreakpointPair(Breakpoint('test', 1), Breakpoint('test', 10), opposing_strands=False)
self.assertFalse(bpp.opposing_strands)
