def test_variants(self):
start = 120000
stop = 121000
x = pileup.Features(json="{}",
build='hg19',
contig='chr1',
start=start,
stop=stop)
assert (x.start == start)
assert (x.stop == stop)
def test_minimal_features_html(self):
w = pileup.Features(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
output = StringIO()
state = dependency_state(w, drop_defaults=True)
embed_minimal_html(output, views=w, drop_defaults=True, state=state)
content = output.getvalue()
assert content.splitlines()[0] == '<!DOCTYPE html>'
def test_embed_features(self):
w = pileup.Features(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
state = dependency_state(w, drop_defaults=True)
data = embed_data(views=w, drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 1
model_names = [s['model_name'] for s in state.values()]
assert 'FeatureModel' in model_names
def ViewFeatures(self, featureRDD, contig, start, end, showPlot=True):
contig_trimmed = contig.lstrip(self.chrPrefix)
# Filter RDD
filtered = featureRDD.transform(lambda r: r.filter(
((r.contigName == contig) | (r.contigName == contig_trimmed))
& (r.start < end) & (r.end > start)))
# convert to GA4GH JSON to be consumed by mango-viz module
json = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.featureRDDtoJSON(
filtered._jvmRdd)
# visualize
if (showPlot):
return pileup.Features(json=json,
build=self.build,
contig=contig,
start=start,
stop=end)
def test_embed_data_two_widgets(self):
w1 = pileup.Variants(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
w2 = pileup.Features(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
jslink((w1, 'start'), (w2, 'start'))
state = dependency_state([w1, w2], drop_defaults=True)
data = embed_data(views=[w1, w2], drop_defaults=True, state=state)
state = data['manager_state']['state']
views = data['view_specs']
assert len(views) == 2
model_names = [s['model_name'] for s in state.values()]
assert 'VariantModel' in model_names
assert 'FeatureModel' in model_names