def test_barcode_split_cornercases(self): fn = ('/pbi/dept/secondary/siv/testdata/' 'pblaa-unittest/Sequel/Phi29/m54008_160219_003234' '.tiny.subreadset.xml') sset = SubreadSet(fn) ssets = sset.split(chunks=3, barcodes=True) self.assertEqual([str(ss.filters) for ss in ssets], ["( bc = [0, 0] )", "( bc = [1, 1] )", "( bc = [2, 2] )"]) sset = SubreadSet(fn) self.assertEqual(len(sset), 15133) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters.addRequirement(bc=[('=', '[2, 2]')]) self.assertEqual(str(sset.filters), "( bc = [2, 2] )") sset.updateCounts() self.assertEqual(len(sset), 4710) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters.addRequirement(bc=[('=', '[2,2]')]) self.assertEqual(str(sset.filters), "( bc = [2,2] )") sset.updateCounts() self.assertEqual(len(sset), 4710)
def test_barcode_split_maxChunks(self): fn = ('/pbi/dept/secondary/siv/testdata/' 'pblaa-unittest/Sequel/Phi29/m54008_160219_003234' '.tiny.subreadset.xml') sset = SubreadSet(fn, skipMissing=True) ssets = sset.split(maxChunks=2, barcodes=True) self.assertEqual( [str(ss.filters) for ss in ssets], ["( bc = [0, 0] )", "( bc = [1, 1] ) OR ( bc = [2, 2] )"]) sset = SubreadSet(fn, skipMissing=True) self.assertEqual(len(sset), 15133) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters = ssets[0].filters self.assertEqual(str(sset.filters), "( bc = [0, 0] )") sset.updateCounts() self.assertEqual(len(sset), 5370) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters = ssets[1].filters self.assertEqual(str(sset.filters), "( bc = [1, 1] ) OR ( bc = [2, 2] )") sset.updateCounts() self.assertEqual(len(sset), 9763)
def test_barcode_split_cornercases(self): fn = ('/pbi/dept/secondary/siv/testdata/' 'pblaa-unittest/Sequel/Phi29/m54008_160219_003234' '.tiny.subreadset.xml') sset = SubreadSet(fn, skipMissing=True) ssets = sset.split(chunks=3, barcodes=True) self.assertEqual( [str(ss.filters) for ss in ssets], ["( bc = [0, 0] )", "( bc = [1, 1] )", "( bc = [2, 2] )"]) sset = SubreadSet(fn, skipMissing=True) self.assertEqual(len(sset), 15133) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters.addRequirement(bc=[('=', '[2, 2]')]) self.assertEqual(str(sset.filters), "( bc = [2, 2] )") sset.updateCounts() self.assertEqual(len(sset), 4710) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters.addRequirement(bc=[('=', '[2,2]')]) self.assertEqual(str(sset.filters), "( bc = [2,2] )") sset.updateCounts() self.assertEqual(len(sset), 4710)
def test_barcode_split_maxChunks(self): fn = ('/pbi/dept/secondary/siv/testdata/' 'pblaa-unittest/Sequel/Phi29/m54008_160219_003234' '.tiny.subreadset.xml') sset = SubreadSet(fn, skipMissing=True) ssets = list(sset.split(maxChunks=2, barcodes=True)) assert [str(ss.filters) for ss in ssets ] == ["( bc = [0, 0] )", "( bc = [1, 1] ) OR ( bc = [2, 2] )"] sset = SubreadSet(fn, skipMissing=True) assert len(sset) == 15133 sset.filters = None assert str(sset.filters) == "" sset.updateCounts() assert len(sset) == 2667562 sset.filters = ssets[0].filters assert str(sset.filters) == "( bc = [0, 0] )" sset.updateCounts() assert len(sset) == 5370 sset.filters = None assert str(sset.filters) == "" sset.updateCounts() assert len(sset) == 2667562 sset.filters = ssets[1].filters assert str(sset.filters) == "( bc = [1, 1] ) OR ( bc = [2, 2] )" sset.updateCounts() assert len(sset) == 9763
def test_barcode_split_cornercases(self): fn = ('/pbi/dept/secondary/siv/testdata/' 'pblaa-unittest/Sequel/Phi29/m54008_160219_003234' '.tiny.subreadset.xml') sset = SubreadSet(fn, skipMissing=True) ssets = list(sset.split(chunks=3, barcodes=True)) assert [str(ss.filters) for ss in ssets ] == ["( bc = [0, 0] )", "( bc = [1, 1] )", "( bc = [2, 2] )"] sset = SubreadSet(fn, skipMissing=True) assert len(sset) == 15133 sset.filters = None assert str(sset.filters) == "" sset.updateCounts() assert len(sset) == 2667562 sset.filters.addRequirement(bc=[('=', '[2, 2]')]) assert str(sset.filters) == "( bc = [2, 2] )" sset.updateCounts() assert len(sset) == 4710 sset.filters = None assert str(sset.filters) == "" sset.updateCounts() assert len(sset) == 2667562 sset.filters.addRequirement(bc=[('=', '[2,2]')]) assert str(sset.filters) == "( bc = [2,2] )" sset.updateCounts() assert len(sset) == 4710
def test_barcode_split_maxChunks(self): fn = ('/pbi/dept/secondary/siv/testdata/' 'pblaa-unittest/Sequel/Phi29/m54008_160219_003234' '.tiny.subreadset.xml') sset = SubreadSet(fn, skipMissing=True) ssets = sset.split(maxChunks=2, barcodes=True) self.assertEqual([str(ss.filters) for ss in ssets], ["( bc = [0, 0] )", "( bc = [1, 1] ) OR ( bc = [2, 2] )"]) sset = SubreadSet(fn, skipMissing=True) self.assertEqual(len(sset), 15133) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters = ssets[0].filters self.assertEqual(str(sset.filters), "( bc = [0, 0] )") sset.updateCounts() self.assertEqual(len(sset), 5370) sset.filters = None self.assertEqual(str(sset.filters), "") sset.updateCounts() self.assertEqual(len(sset), 2667562) sset.filters = ssets[1].filters self.assertEqual(str(sset.filters), "( bc = [1, 1] ) OR ( bc = [2, 2] )") sset.updateCounts() self.assertEqual(len(sset), 9763)