def test_filter_reference_contigs(self): ds2 = ReferenceSet(data.getRef()) self.assertEqual(len(list(ds2.refNames)), 59) filt = Filters() filt.addRequirement(id=[('==', 'E.faecalis.1')]) ds2.addFilters(filt) self.assertEqual(str(ds2.filters), "( id == E.faecalis.1 )") self.assertEqual(len(ds2.refNames), 1) self.assertEqual(len(list(ds2.records)), 1) ds2.disableFilters() self.assertEqual(len(list(ds2.refNames)), 59) self.assertEqual(len(list(ds2.records)), 59) ds2.enableFilters() self.assertEqual(len(list(ds2.refNames)), 1) self.assertEqual(len(list(ds2.records)), 1)
def test_loading_reference(self): log.info('Opening Reference') r = ReferenceSet(data.getRef()).toExternalFiles()[0] log.info('Done Opening Reference') log.info('Opening AlignmentSet') d = AlignmentSet(data.getBam(), referenceFastaFname=r) log.info('Done Opening AlignmentSet') bfile = openIndexedAlignmentFile(data.getBam(), referenceFastaFname=r) self.assertTrue(bfile.isReferenceLoaded) for res in d.resourceReaders(): self.assertTrue(res.isReferenceLoaded) aln = AlignmentSet(data.getBam()) aln.addReference(r) for res in aln.resourceReaders(): self.assertTrue(res.isReferenceLoaded)
def test_filter_reference_contigs(self): ds2 = ReferenceSet(data.getRef()) assert len(list(ds2.refNames)) == 59 assert len(list(ds2.records)) == len(ds2.index) filt = Filters() filt.addRequirement(id=[('==', 'E.faecalis.1')]) ds2.addFilters(filt) assert str(ds2.filters) == "( id == E.faecalis.1 )" assert len(ds2.refNames) == 1 assert len(list(ds2.records)) == 1 assert len(list(ds2.records)) == len(ds2.index) ds2.disableFilters() assert len(list(ds2.refNames)) == 59 assert len(list(ds2.records)) == 59 assert len(list(ds2.records)) == len(ds2.index) ds2.enableFilters() assert len(list(ds2.refNames)) == 1 assert len(list(ds2.records)) == 1 assert len(list(ds2.records)) == len(ds2.index)