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_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_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]