Python ReferenceRegion.ReferenceRegion Examples

Example #1

File: adamContext_test.py Project: yyz940922/adam

    def test_load_indexed_bam(self):

        testFile = self.resourceFile("indexed_bams/sorted.bam")
        ac = ADAMContext(self.ss)

        reads = ac.loadIndexedBam(testFile,
                                  [ReferenceRegion("chr2", 100, 101),
                                   ReferenceRegion("3", 10, 17)])

        self.assertEqual(reads.toDF().count(), 2)

Example #2

File: alignmentRecordDataset_test.py Project: qzhqzh/adam

    def test_filterByOverlappingRegions(self):

        readsPath = self.resourceFile("unsorted.sam")
        ac = ADAMContext(self.ss)

        reads = ac.loadAlignments(readsPath)

        querys = [ReferenceRegion("chr2", 1, 400),
                    ReferenceRegion("3", 1, 100)]

        filtered = reads.filterByOverlappingRegions(querys)
        self.assertEqual(filtered.toDF().count(), 2)