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# http://www.apache.org/licenses/LICENSE-2.0
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r"""
========
Variants
========
.. currentmodule:: bdgenomics.mango.variants
.. autosummary::
:toctree: _generate/
VariantSummary
"""
import bdgenomics.mango.pileup as pileup
from bdgenomics.mango.pileup.track import *
from bdgenomics.adam.adamContext import ADAMContext
from .utils import *
[docs]class VariantSummary(object):
""" VariantSummary class.
VariantSummary provides scrollable visualization of variants based on genomic regions.
"""
[docs] def __init__(self, ac, dataset):
"""
Initializes a GenomicDataset viz class.
Args:
:param ac: bdgenomics.adamContext.ADAMContext
:param dataset: bdgenomics.adam.ds.VariantDataset
"""
self.ac = ac
self.dataset = dataset
# Takes a bdgenomics.adam.VariantContextRDD and visualizes results
def viewPileup(self, contig, start, end, reference = 'hg19', label = "Variants", showPlot = True):
"""
Visualizes a portion of this VariantRDD 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 variant track
showPlot: Disables widget, used for testing. Default is true.
Returns:
pileup view for variants
"""
contig_trimmed, contig_full = formatContig(contig)
# Filter RDD
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.variantDatasetToJSON(filtered._jvmDataset)
# visualize
if (showPlot):
# make variant track
tracks=[Track(viz="variants", label=label, source=pileup.sources.GA4GHVariantJson(json))]
locus="%s:%i-%i" % (contig, start, end)
return pileup.PileupViewer(locus=locus, reference=reference, tracks=tracks)