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)
