def test_reads(self):
start = 120000
stop = 121000
x = pileup.Reads(json="{}",
build='hg19',
contig='chr17',
start=start,
stop=stop)
assert (x.start == start)
assert (x.stop == stop)
def test_minimal_reads_html(self):
w = pileup.Reads(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_alignments(self):
w = pileup.Reads(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 'ReadsModel' in model_names
def test_snippet(self):
class Parser(HTMLParser):
state = 'initial'
states = []
def handle_starttag(self, tag, attrs):
attrs = dict(attrs)
if tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-state+json":
self.state = 'widget-state'
self.states.append(self.state)
elif tag == 'script' and attrs.get(
'type',
'') == "application/vnd.jupyter.widget-view+json":
self.state = 'widget-view'
self.states.append(self.state)
def handle_endtag(self, tag):
self.state = 'initial'
def handle_data(self, data):
if self.state == 'widget-state':
manager_state = json.loads(data)['state']
assert len(manager_state) == 2
self.states.append('check-widget-state')
elif self.state == 'widget-view':
view = json.loads(data)
assert isinstance(view, dict)
self.states.append('check-widget-view')
w = pileup.Reads(json="{}",
build='hg19',
contig='chr1',
start=1,
stop=20)
state = dependency_state(w, drop_defaults=True)
snippet = embed_snippet(views=w, drop_defaults=True, state=state)
parser = Parser()
parser.feed(snippet)
assert parser.states == [
'widget-state', 'check-widget-state', 'widget-view',
'check-widget-view'
]
def ViewAlignments(self,
alignmentRecordRDD,
contig,
start,
end,
showPlot=True):
contig_trimmed = contig.lstrip(self.chrPrefix)
# Filter RDD
filtered = alignmentRecordRDD.transform(lambda r: r.filter(
((r.contigName == contig) | (r.contigName == contig_trimmed))
& (r.start < end) & (r.end > start) & (r.readMapped)))
# convert to GA4GH JSON to be consumed by mango-viz module
json = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.alignmentRecordRDDtoJSON(
filtered._jvmRdd)
# visualize
if (showPlot):
return pileup.Reads(json=json,
build=self.build,
contig=contig,
start=start,
stop=end)