test_application.py

#
# Licensed to Big Data Genomics (BDG) under one
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# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
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#

import unittest
import bdgenomics.mango.pileup as pileup


class MangoVizTest(unittest.TestCase):

    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_features(self):
        track = pileup.Track(viz="features", label="myFeatures", source=pileup.sources.GA4GHFeatureJson('{}'))

        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_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_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_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_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)


# Run tests
if __name__ == '__main__':
    unittest.main()