def test_multi_movie_split_zmws_existing_filters(self):
N_RECORDS = 1745161
test_file_1 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2372215/0007/Analysis_Results/m150404_101626_42"
"267_c100807920800000001823174110291514_s1_p0.al"
"l.subreadset.xml")
test_file_2 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2590980/0008/Analysis_Results/m141115_075238_et"
"han_c100699872550000001823139203261572_s1_p0.al"
"l.subreadset.xml")
ds1 = SubreadSet(test_file_1, test_file_2)
# used to get total:
#self.assertEqual(sum(1 for _ in ds1), N_RECORDS)
self.assertEqual(len(ds1), N_RECORDS)
ds1.filters.addRequirement(
movie=[('=',
'm150404_101626_42267_c100807920800000001823174110291514_s1_p0'),
('=',
'm141115_075238_ethan_c100699872550000001823139203261572_s1_p0')],
zm=[('>', 10), ('>', 127900)])
ds1.filters.mapRequirement(
zm=[('<', 10000), ('<', 140000)])
FILT_RECORDS = 117776
self.assertEqual(len(ds1), FILT_RECORDS)
ds1._index = None
ds1.updateCounts()
self.assertEqual(len(ds1), FILT_RECORDS)
dss = ds1.split(chunks=1, zmws=True)
self.assertEqual(len(dss), 1)
self.assertEqual(len(dss[0]), FILT_RECORDS)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
FILT_RECORDS)
dss = ds1.split(chunks=12, zmws=True)
self.assertEqual(len(dss), 12)
self.assertEqual(sum([len(ds_) for ds_ in dss]),
FILT_RECORDS)
self.assertEqual(
dss[0].zmwRanges,
[('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
11, 1515)])
self.assertEqual(
dss[-1].zmwRanges,
[('m141115_075238_ethan_c100699872550000001823139203261572_s1_p0',
137634, 139999)])
def test_multi_movie_split_zmws_existing_filters(self):
N_RECORDS = 1745161
test_file_1 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2372215/0007/Analysis_Results/m150404_101626_42"
"267_c100807920800000001823174110291514_s1_p0.al"
"l.subreadset.xml")
test_file_2 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2590980/0008/Analysis_Results/m141115_075238_et"
"han_c100699872550000001823139203261572_s1_p0.al"
"l.subreadset.xml")
ds1 = SubreadSet(test_file_1, test_file_2)
# used to get total:
#self.assertEqual(sum(1 for _ in ds1), N_RECORDS)
self.assertEqual(len(ds1), N_RECORDS)
ds1.filters.addRequirement(movie=[
('=',
'm150404_101626_42267_c100807920800000001823174110291514_s1_p0'),
('=',
'm141115_075238_ethan_c100699872550000001823139203261572_s1_p0')
],
zm=[('>', 10), ('>', 127900)])
ds1.filters.mapRequirement(zm=[('<', 10000), ('<', 140000)])
FILT_RECORDS = 117776
self.assertEqual(len(ds1), FILT_RECORDS)
ds1._index = None
ds1.updateCounts()
self.assertEqual(len(ds1), FILT_RECORDS)
dss = ds1.split(chunks=1, zmws=True)
self.assertEqual(len(dss), 1)
self.assertEqual(len(dss[0]), FILT_RECORDS)
self.assertEqual(sum([len(ds_) for ds_ in dss]), FILT_RECORDS)
dss = ds1.split(chunks=12, zmws=True)
self.assertEqual(len(dss), 12)
self.assertEqual(sum([len(ds_) for ds_ in dss]), FILT_RECORDS)
self.assertEqual(
dss[0].zmwRanges,
[('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
11, 1515)])
self.assertEqual(
dss[-1].zmwRanges,
[('m141115_075238_ethan_c100699872550000001823139203261572_s1_p0',
137634, 139999)])
def test_multi_movie_split_zmws_existing_simple_filters(self):
N_RECORDS = 1745161
test_file_1 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2372215/0007/Analysis_Results/m150404_101626_42"
"267_c100807920800000001823174110291514_s1_p0.al"
"l.subreadset.xml")
test_file_2 = ("/pbi/dept/secondary/siv/testdata/SA3-DS/lambda/"
"2590980/0008/Analysis_Results/m141115_075238_et"
"han_c100699872550000001823139203261572_s1_p0.al"
"l.subreadset.xml")
ds1 = SubreadSet(test_file_1, test_file_2)
# used to get total:
#assert sum(1 for _ in ds1) == N_RECORDS
assert len(ds1) == N_RECORDS
ds1.filters.addRequirement(rq=[('>', '0.7'), ('<', '0.5')])
FILT_RECORDS = 1732613
assert len(ds1) == FILT_RECORDS
ds1._index = None
ds1.updateCounts()
assert len(ds1) == FILT_RECORDS
dss = list(ds1.split(chunks=1, zmws=True))
dss[0]._index = None
dss[0].updateCounts()
assert len(dss) == 1
assert len(dss[0]) == FILT_RECORDS
assert sum([len(ds_) for ds_ in dss]) == FILT_RECORDS
dss = list(ds1.split(chunks=12, zmws=True))
assert len(dss) == 12
assert sum([len(ds_) for ds_ in dss]) == FILT_RECORDS
assert dss[0].zmwRanges == [
('m150404_101626_42267_c100807920800000001823174110291514_s1_p0',
7, 22073)
]
assert dss[-1].zmwRanges == [
('m141115_075238_ethan_c100699872550000001823139203261572_s1_p0',
127695, 163468)
]
