def test_fragment_with_duplicate_in_pair_1_no_discard(self):
# Ensure the reducer catches a fragment duplicate of pair[0]
p = list(test_utils.pair1())
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
p = test_utils.erase_read2(p)
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__reducer.discard_duplicates = False
self.__reducer.reduce(self.__ctx)
# now ensure that both were emitted, but the fragment is marked as duplicate
self.__ensure_pair1_emitted()
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(3, len(self.__ctx.emitted.values()[0])) # 3 SAM records associated with the key (for the pair)
# make sure we have a read with the duplicate flag set
regexp = "(\d+)\s+.*"
flags = [ int(re.match(regexp, value).group(1)) for value in self.__ctx.emitted.values()[0] ]
dup_flags = [ flag for flag in flags if flag & sam_flags.SAM_FDP ]
self.assertEqual(1, len(dup_flags))
f = dup_flags[0]
self.assertTrue( f & sam_flags.SAM_FR1 > 0 ) # ensure the duplicate read is r1
self.assertTrue( f & sam_flags.SAM_FPD == 0 ) # ensure the duplicate read is unpaired
# check counter
self.assertFalse(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_unmapped2(self):
p = test_utils.pair1()
p[1].set_mapped(False)
p[0].set_mate_mapped(False)
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
self.assertEqual(2, len(self.__ctx.emitted.values()[0]))
def test_emit_on_left_key(self):
# load pair 1
p = test_utils.pair1()
# use the first read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
self.__ensure_only_pair1_emitted()
def test_duplicate_fragments_read1(self):
# load pair 1
p = list(test_utils.pair1())
p = test_utils.erase_read2(p)
p0 = p[0]
# insert the pair into the context, twice
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(
1, len(self.__ctx.emitted.values()
[0])) # only one SAM record associated with the key
short_name = p0.get_name()[0:-2]
self.assertEqual(short_name, self.__ctx.emitted.keys()[0])
self.assertTrue(
re.match("\d+\s+%s\s+%d\s+.*" % (p0.tid, p0.pos),
self.__ctx.emitted[short_name][0]))
# check counter
self.assertFalse(
self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(
self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_no_emit_on_right_key(self):
# load pair 1
p = test_utils.pair1()
# use the SECOND read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
self.__reducer.reduce(self.__ctx)
# we should have no output
self.assertEqual(0, len(self.__ctx.emitted.keys()))
def setUp(self): self.ctx = map_context(None, None) self.count_group = "Test" self.logger = SavingLogger() self.monitor = HadoopEventMonitor(self.count_group, self.logger, self.ctx) self.link = MarkDuplicatesEmitter(self.ctx, self.monitor) self.pair1 = test_utils.pair1() self.pair2 = test_utils.pair2()
def test_unmapped2(self):
p = test_utils.pair1()
p[1].set_mapped(False)
p[0].set_mate_mapped(False)
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
self.assertEqual(2, len(self.__ctx.emitted.values()[0]))
def test_no_emit_on_right_key(self):
# load pair 1
p = test_utils.pair1()
# use the SECOND read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
self.__reducer.reduce(self.__ctx)
# we should have no output
self.assertEqual(0, len(self.__ctx.emitted.keys()))
def test_emit_on_left_key(self):
# load pair 1
p = test_utils.pair1()
# use the first read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
self.__ensure_only_pair1_emitted()
def setUp(self):
self.ctx = map_context(None, None)
self.count_group = "Test"
self.logger = SavingLogger()
self.monitor = HadoopEventMonitor(self.count_group, self.logger,
self.ctx)
self.link = MarkDuplicatesEmitter(self.ctx, self.monitor)
self.pair1 = test_utils.pair1()
self.pair2 = test_utils.pair2()
def __ensure_pair1_emitted(self):
p = test_utils.pair1()
# Now we expect a SAM entry for each of the two pairs.
# At the moment, the SAM formatter emits the read name as the key, and the
# rest of the SAM record as the value. Remember that the protobuff serialization
# removes the read number ("/1" or "/2") from the read name.
short_name = p[0].get_name()[0:-2] # mapping name without the read number
self.assertTrue( self.__ctx.emitted.has_key(short_name) )
self.assertTrue(len(self.__ctx.emitted[short_name]) >= 2 ) # at least two SAM records emitted
def test_unmapped1(self):
p = test_utils.pair1()
p[0].set_mapped(False)
p[1].set_mate_mapped(False)
# Having an unmapped read before a mapped read is not allowed. This should
# raise an exception
# The key is meaningless
self.__ctx.add_value(test_utils.make_key(p[1]), proto.serialize_pair(p))
self.assertRaises(ValueError, self.__reducer.reduce, self.__ctx)
def test_unmapped1(self):
p = test_utils.pair1()
p[0].set_mapped(False)
p[1].set_mate_mapped(False)
# Having an unmapped read before a mapped read is not allowed. This should
# raise an exception
# The key is meaningless
self.__ctx.add_value(test_utils.make_key(p[1]),
proto.serialize_pair(p))
self.assertRaises(ValueError, self.__reducer.reduce, self.__ctx)
def __ensure_pair1_emitted(self):
p = test_utils.pair1()
# Now we expect a SAM entry for each of the two pairs.
# At the moment, the SAM formatter emits the read name as the key, and the
# rest of the SAM record as the value. Remember that the protobuff serialization
# removes the read number ("/1" or "/2") from the read name.
short_name = p[0].get_name()[
0:-2] # mapping name without the read number
self.assertTrue(self.__ctx.emitted.has_key(short_name))
self.assertTrue(len(self.__ctx.emitted[short_name]) >=
2) # at least two SAM records emitted
def __ensure_only_pair1_emitted(self):
self.__ensure_pair1_emitted()
p = test_utils.pair1()
short_name = p[0].get_name()[0:-2] # mapping name without the read number
self.assertEqual( [short_name], self.__ctx.emitted.keys() )
self.assertEqual(2, len(self.__ctx.emitted[short_name])) # two SAM records emitted
regexp = "\d+\s+%s\s+(\d+)\s+.*" % p[0].tid # all reads have the same tid. Match the position
emitted_positions = map(lambda sam: int(*re.match(regexp, sam).groups(1)), self.__ctx.emitted[short_name])
self.assertEqual( [p[0].pos, p[1].pos], sorted(emitted_positions) ) # ensure we have both positions
emitted_flags = map(lambda sam: int(*re.match("(\d+).*", sam).groups(1)), self.__ctx.emitted[short_name])
# ensure all the reads we found are flagged as mapped
self.assertTrue( all(map(lambda flag: flag & (sam_flags.SAM_FSU | sam_flags.SAM_FMU) == 0, emitted_flags)) )
def test_duplicate_pairs_right_key(self):
# Two identical pairs on the right key
# Ensure nothing is emitted
p = test_utils.pair1()
# use the first read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING) # add it twice
self.__reducer.reduce(self.__ctx)
self.assertEqual(0, len(self.__ctx.emitted.keys()))
# check counter
if self.__ctx.counters.has_key(self.__pair_counter_name()):
self.assertEqual(0, self.__ctx.counters[self.__pair_counter_name()])
if self.__ctx.counters.has_key(self.__frag_counter_name()):
self.assertEqual(0, self.__ctx.counters[self.__frag_counter_name()])
def test_fragment_with_duplicate_in_pair_1(self):
# Ensure the reducer catches a fragment duplicate of pair[0]
p = list(test_utils.pair1())
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
test_utils.erase_read2(p)
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
# now ensure that the pair was emitted, but not the fragment
self.__ensure_only_pair1_emitted()
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(2, len(self.__ctx.emitted.values()[0])) # two SAM records associated with the key (for the pair)
# check counter
self.assertFalse(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_duplicate_pairs(self):
# Two identical pairs. Ensure only one is emitted
p = test_utils.pair1()
# use the first read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p)) # add it twice
self.__reducer.reduce(self.__ctx)
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(2, len(self.__ctx.emitted.values()[0])) # two SAM records associated with the same key
self.__ensure_only_pair1_emitted()
# check counter
if self.__ctx.counters.has_key(self.__frag_counter_name()):
self.assertEqual(0, self.__ctx.counters[self.__frag_counter_name()])
self.assertTrue(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__pair_counter_name()])
def test_duplicate_pairs_right_key(self):
# Two identical pairs on the right key
# Ensure nothing is emitted
p = test_utils.pair1()
# use the first read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
self.__ctx.add_value(test_utils.make_key(p[1]),
PAIR_STRING) # add it twice
self.__reducer.reduce(self.__ctx)
self.assertEqual(0, len(self.__ctx.emitted.keys()))
# check counter
if self.__ctx.counters.has_key(self.__pair_counter_name()):
self.assertEqual(0,
self.__ctx.counters[self.__pair_counter_name()])
if self.__ctx.counters.has_key(self.__frag_counter_name()):
self.assertEqual(0,
self.__ctx.counters[self.__frag_counter_name()])
def test_fragment_with_duplicate_in_pair_2(self):
# Ensure the reducer catches a fragment duplicate of pair[1].
p = list(test_utils.pair1())
# Insert the pair into the context
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
# Remove the first read from the pair, reorder so that the None is at index 1,
# the serialize and insert into the context.
test_utils.erase_read1(p)
self.__ctx.add_value(test_utils.make_key(p[1]), proto.serialize_pair( (p[1], None) ))
self.__reducer.reduce(self.__ctx)
# now ensure that nothing was emitted. The pair isn't emitted because
# the key refers to read2, and the fragment isn't emitted because it's a duplicate of
# the one in the pair.
self.assertEqual(0, len(self.__ctx.emitted.keys()))
# check counter
self.assertFalse(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_duplicate_fragments_read1(self):
# load pair 1
p = list(test_utils.pair1())
p = test_utils.erase_read2(p)
p0 = p[0]
# insert the pair into the context, twice
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(1, len(self.__ctx.emitted.values()[0])) # only one SAM record associated with the key
short_name = p0.get_name()[0:-2]
self.assertEqual(short_name, self.__ctx.emitted.keys()[0])
self.assertTrue( re.match("\d+\s+%s\s+%d\s+.*" % (p0.tid, p0.pos), self.__ctx.emitted[short_name][0]) )
# check counter
self.assertFalse(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_duplicate_pairs_no_discard(self):
# Two identical pairs. Ensure only one is emitted
p = test_utils.pair1()
# use the first read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p)) # add it twice
self.__reducer.discard_duplicates = False
self.__reducer.reduce(self.__ctx)
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(4, len(self.__ctx.emitted.values()[0])) # four SAM records associated with the same key
flags = map(lambda sam: int(*re.match("(\d+).*", sam).groups(1)), self.__ctx.emitted.values()[0])
# ensure we have two marked as duplicates
self.assertEqual(2, len(filter(lambda flag: flag & sam_flags.SAM_FDP, flags)) )
# ensure we have two NOT marked as duplicates
self.assertEqual(2, len(filter(lambda flag: flag & sam_flags.SAM_FDP == 0, flags)) )
# check counter
if self.__ctx.counters.has_key(self.__frag_counter_name()):
self.assertEqual(0, self.__ctx.counters[self.__frag_counter_name()])
self.assertTrue(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__pair_counter_name()])
def test_fragment_with_duplicate_in_pair_1(self):
# Ensure the reducer catches a fragment duplicate of pair[0]
p = list(test_utils.pair1())
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
test_utils.erase_read2(p)
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
self.__reducer.reduce(self.__ctx)
# now ensure that the pair was emitted, but not the fragment
self.__ensure_only_pair1_emitted()
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(2, len(
self.__ctx.emitted.values()
[0])) # two SAM records associated with the key (for the pair)
# check counter
self.assertFalse(
self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(
self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_duplicate_pairs(self):
# Two identical pairs. Ensure only one is emitted
p = test_utils.pair1()
# use the first read to create the map-reduce key
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p)) # add it twice
self.__reducer.reduce(self.__ctx)
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(
2, len(self.__ctx.emitted.values()
[0])) # two SAM records associated with the same key
self.__ensure_only_pair1_emitted()
# check counter
if self.__ctx.counters.has_key(self.__frag_counter_name()):
self.assertEqual(0,
self.__ctx.counters[self.__frag_counter_name()])
self.assertTrue(self.__ctx.counters.has_key(
self.__pair_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__pair_counter_name()])
def test_fragment_with_duplicate_in_pair_2(self):
# Ensure the reducer catches a fragment duplicate of pair[1].
p = list(test_utils.pair1())
# Insert the pair into the context
self.__ctx.add_value(test_utils.make_key(p[1]), PAIR_STRING)
# Remove the first read from the pair, reorder so that the None is at index 1,
# the serialize and insert into the context.
test_utils.erase_read1(p)
self.__ctx.add_value(test_utils.make_key(p[1]),
proto.serialize_pair((p[1], None)))
self.__reducer.reduce(self.__ctx)
# now ensure that nothing was emitted. The pair isn't emitted because
# the key refers to read2, and the fragment isn't emitted because it's a duplicate of
# the one in the pair.
self.assertEqual(0, len(self.__ctx.emitted.keys()))
# check counter
self.assertFalse(
self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(
self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_fragment_with_duplicate_in_pair_1_no_discard(self):
# Ensure the reducer catches a fragment duplicate of pair[0]
p = list(test_utils.pair1())
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
p = test_utils.erase_read2(p)
self.__ctx.add_value(test_utils.make_key(p[0]),
proto.serialize_pair(p))
self.__reducer.discard_duplicates = False
self.__reducer.reduce(self.__ctx)
# now ensure that both were emitted, but the fragment is marked as duplicate
self.__ensure_pair1_emitted()
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(3, len(
self.__ctx.emitted.values()
[0])) # 3 SAM records associated with the key (for the pair)
# make sure we have a read with the duplicate flag set
regexp = "(\d+)\s+.*"
flags = [
int(re.match(regexp, value).group(1))
for value in self.__ctx.emitted.values()[0]
]
dup_flags = [flag for flag in flags if flag & sam_flags.SAM_FDP]
self.assertEqual(1, len(dup_flags))
f = dup_flags[0]
self.assertTrue(
f & sam_flags.SAM_FR1 > 0) # ensure the duplicate read is r1
self.assertTrue(
f
& sam_flags.SAM_FPD == 0) # ensure the duplicate read is unpaired
# check counter
self.assertFalse(
self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(
self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_duplicate_fragments_read1_no_discard(self):
# load pair 1 and erase its second read
p = list(test_utils.pair1())
p = test_utils.erase_read2(p)
p0 = p[0]
# insert the pair into the context, twice
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__ctx.add_value(test_utils.make_key(p[0]), proto.serialize_pair(p))
self.__reducer.discard_duplicates = False
self.__reducer.reduce(self.__ctx)
self.assertEqual(1, len(self.__ctx.emitted.keys()))
self.assertEqual(2, len(self.__ctx.emitted.values()[0])) # Two SAM records associated with the key
short_name = p0.get_name()[0:-2]
self.assertEqual(short_name, self.__ctx.emitted.keys()[0])
flags = map(lambda sam: int(*re.match("(\d+).*", sam).groups(1)), self.__ctx.emitted.values()[0])
# ensure we have one marked as duplicate
self.assertEqual(1, len(filter(lambda flag: flag & sam_flags.SAM_FDP, flags)) )
# and ensure we have one NOT marked as duplicates
self.assertEqual(1, len(filter(lambda flag: flag & sam_flags.SAM_FDP == 0, flags)) )
# check counter
self.assertFalse(self.__ctx.counters.has_key(self.__pair_counter_name()))
self.assertTrue(self.__ctx.counters.has_key(self.__frag_counter_name()))
self.assertEqual(1, self.__ctx.counters[self.__frag_counter_name()])
def test_empty_read1(self):
# Ensure the reducer raises an exception if the pair[0] is None
p = test_utils.erase_read1(list(test_utils.pair1()))
self.__ctx.add_value(test_utils.make_key(p[1]),
proto.serialize_pair(p))
self.assertRaises(ValueError, self.__reducer.reduce, self.__ctx)
def test_empty_read1(self):
# Ensure the reducer raises an exception if the pair[0] is None
p = test_utils.erase_read1(list(test_utils.pair1()))
self.__ctx.add_value(test_utils.make_key(p[1]), proto.serialize_pair(p))
self.assertRaises(ValueError, self.__reducer.reduce, self.__ctx)
