def test_embed_data_two_widgets(self):
feature_track = pileup.Track(
viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
variant_track = pileup.Track(
viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
w1 = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[feature_track])
w2 = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[variant_track])
jslink((w1, 'reference'), (w2, 'reference'))
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()]
widget_names = list(
filter(lambda x: x == 'PileupViewerModel', model_names))
assert len(widget_names) == 2
def viewPileup(self, contig, start, end, reference = 'hg19', label = "Features", showPlot = True):
"""
Visualizes a portion of this FeatureDataset in a scrollable pileup widget
Args:
:param contig: contig of locus to view
:param start: start position of locus to view
:param end: end position of locus to view
reference: genome build. Default is hg19
label: name of feature track
showPlot: Disables widget, used for testing. Default is true.
Returns:
pileup view for features
"""
contig_trimmed, contig_full = formatContig(contig)
# Filter dataset
filtered = self.dataset.transform(lambda r: r.filter(((r.referenceName == contig_full) | (r.referenceName == contig_trimmed))
& (r.start < end) & (r.end > start)))
# convert to GA4GH JSON to be consumed by mango-pileup module
json = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.featureDatasetToJSON(filtered._jvmRdd)
# visualize
if (showPlot):
# make feature track
tracks=[Track(viz="features", label=label, source=pileup.sources.GA4GHFeatureJson(json))]
locus="%s:%i-%i" % (contig, start, end)
return pileup.PileupViewer(locus=locus, reference=reference, tracks=tracks)
def test_visualization(self):
dataframe = read_vcf(self.exampleFile(filename))
assert(dataframe._pileup_visualization == "variantJson")
tracks=[Track(viz="variants", label="my variants", source=pileup.sources.DataFrameSource(dataframe))]
reads = pileup.PileupViewer(chrom="chr22",start=10436,stop=10564, reference="hg19", tracks=tracks)
assert(str(type(reads)) == '<class \'bdgenomics.mango.pileup.pileupViewer.PileupViewer\'>')
assert(reads.chrom == 'chr22')
def viewPileup(self,
contig,
start,
end,
reference='hg19',
label="Reads",
multipleGroupNames=False,
showPlot=True):
"""
Visualizes a portion of this AlignmentDataset in a scrollable pileup widget
Args:
:param contig: contig of locus to view
:param start: start position of locus to view
:param end: end position of locus to view
:param reference: genome build. Default is hg19
:param label: name of alignment track
:param multipleGroupName: determines whether to different show tracks for each group name.
If false, coalesces into one track.
:param showPlot: Disables widget, used for testing. Default is true.
Returns:
pileup view for alignments
"""
contig_trimmed = contig.lstrip(CHR_PREFIX)
# Filter Dataset
filtered = self.dataset.transform(lambda r: r.filter(
((r.referenceName == contig) | (r.referenceName == contig_trimmed))
& (r.start < end) & (r.end > start) & (r.readMapped)))
# convert to GA4GH JSON to be consumed by mango-viz module
json_map = self.ac._jvm.org.bdgenomics.mango.converters.GA4GHutil.alignmentRecordDatasetToJSON(
filtered._jvmRdd, multipleGroupNames)
# visualize
if (showPlot):
# make pileup tracks
tracks = []
# iterate through all group names and make a track for each.
for groupName in json_map:
# set label if only one track. Otherwise, set to group names.
thisLabel = groupName if multipleGroupNames else label
# create new track for this recordGroupName. files with unspecified recordGroup name
# have a default label of "1"
track = Track(viz="pileup",
label=thisLabel,
source=pileup.sources.GA4GHAlignmentJson(
json_map[groupName]))
tracks.append(track)
locus = "%s:%i-%i" % (contig, start, end)
return pileup.PileupViewer(locus=locus,
reference=reference,
tracks=tracks)
def test_pileup(self):
track = pileup.Track(viz="pileup",
label="myReads",
source=pileup.sources.GA4GHAlignmentJson('{}'))
x = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_variants(self):
track = pileup.Track(viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
x = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_genotypes(self):
track = pileup.Track(viz="genotypes",
label="myGenotypes",
source=pileup.sources.VcfDataSource('{}'))
x = pileup.PileupViewer(locus="chr22:21340030-21340150",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_toSVG(self):
track = pileup.Track(
viz="genes",
label="myGenes",
source=pileup.sources.BigBedDataSource('fakeGenes.bb'))
x = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[track])
x.getSVG()
def test_genes(self):
track = pileup.Track(
viz="genes",
label="myGenes",
source=pileup.sources.BigBedDataSource('fakeGenes.bb'))
x = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_features(self):
track = pileup.Track(viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
x = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[track])
assert (x.reference == 'hg19')
assert (x.tracks[0] == track)
def test_minimal_pileup_html(self):
track = pileup.Track(viz="pileup",
label="myReads",
source=pileup.sources.GA4GHAlignmentJson('{}'))
w = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
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_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')
track = pileup.Track(viz="variants",
label="myVariants",
source=pileup.sources.GA4GHVariantJson('{}'))
w = pileup.PileupViewer(chrom="chr17",
start=1,
stop=250,
reference="hg19",
tracks=[track])
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 test_embed_pileup(self):
track = pileup.Track(viz="features",
label="myFeatures",
source=pileup.sources.GA4GHFeatureJson('{}'))
w = pileup.PileupViewer(locus="chr17:1-250",
reference="hg19",
tracks=[track])
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 'PileupViewerModel' in model_names
