def test_chain_sorted__mixed_contents():
sequence_a = (3, 4, 8)
sequence_c = (0, 1, 6)
sequence_b = (2, 5, 7)
expected = (0, 1, 2, 3, 4, 5, 6, 7, 8)
result = tuple(utils.chain_sorted(sequence_a, sequence_b, sequence_c))
assert_equal(expected, result)
def test_chain_sorted__mixed_length_contents():
sequence_a = (1, )
sequence_c = (0, 2)
sequence_b = ()
expected = (0, 1, 2)
result = tuple(utils.chain_sorted(sequence_a, sequence_b, sequence_c))
assert_equal(expected, result)
def test_chain_sorted__mixed_length_contents():
sequence_a = (1,)
sequence_c = (0, 2)
sequence_b = ()
expected = (0, 1, 2)
result = tuple(utils.chain_sorted(sequence_a, sequence_b, sequence_c))
assert_equal(expected, result)
def test_chain_sorted__mixed_contents():
sequence_a = (3, 4, 8)
sequence_c = (0, 1, 6)
sequence_b = (2, 5, 7)
expected = (0, 1, 2, 3, 4, 5, 6, 7, 8)
result = tuple(utils.chain_sorted(sequence_a, sequence_b, sequence_c))
assert_equal(expected, result)
def test_chain_sorted__identical_objects_are_preserved():
object_a = [1]
object_b = [1]
assert object_a is not object_b
expected = (object_a, object_b)
result = tuple(utils.chain_sorted([object_a], [object_b]))
assert_equal(expected, result)
assert(object_a is result[0] or object_a is result[1])
assert(object_b is result[0] or object_b is result[1])
def test_chain_sorted__identical_objects_are_preserved():
object_a = [1]
object_b = [1]
assert object_a is not object_b
expected = (object_a, object_b)
result = tuple(utils.chain_sorted([object_a], [object_b]))
assert_equal(expected, result)
assert (object_a is result[0] or object_a is result[1])
assert (object_b is result[0] or object_b is result[1])
def run(self, _):
handles = []
try:
sequences = []
for fpath in self.input_files:
handle = pysam.Samfile(fpath)
handles.append(handle)
sequence = izip_longest(handle, (), fillvalue=fpath)
sequences.append(sequence)
position = 0
records = chain_sorted(*sequences, key=self._key_by_tid_pos)
observed_reads = collections.defaultdict(list)
for (record, fpath) in records:
if record.pos != position:
self._process_reads(observed_reads, self.output_files)
observed_reads.clear()
position = record.pos
elif record.is_unmapped:
break
# Ignore supplementary / secondary alignments
if not record.flag & 0x900:
key = (record.is_reverse, record.qname, record.seq,
record.qual)
observed_reads[key].append(fpath)
self._process_reads(observed_reads, self.output_files)
# Everything is ok, touch the output files
for fpath in self.output_files:
make_dirs(os.path.dirname(fpath))
with open(fpath, "w"):
pass
finally:
for handle in handles:
handle.close()
def run(self, _):
handles = []
try:
sequences = []
for fpath in self.input_files:
handle = pysam.Samfile(fpath)
handles.append(handle)
sequence = izip_longest(handle, (), fillvalue=fpath)
sequences.append(sequence)
position = 0
records = chain_sorted(*sequences, key=self._key_by_tid_pos)
observed_reads = collections.defaultdict(list)
for (record, fpath) in records:
if record.pos != position:
self._process_reads(observed_reads, self.output_files)
observed_reads.clear()
position = record.pos
elif record.is_unmapped:
break
# Ignore supplementary / secondary alignments
if not record.flag & 0x900:
key = (record.is_reverse, record.qname,
record.seq, record.qual)
observed_reads[key].append(fpath)
self._process_reads(observed_reads, self.output_files)
# Everything is ok, touch the output files
for fpath in self.output_files:
make_dirs(os.path.dirname(fpath))
with open(fpath, "w"):
pass
finally:
for handle in handles:
handle.close()
def test_chain_sorted__mixed_contents__reverse():
sequence_a = (-2, -3, -5)
sequence_b = (0, -1, -4)
expected = (0, -1, -2, -3, -4, -5)
result = tuple(utils.chain_sorted(sequence_a, sequence_b, reverse=True))
assert_equal(expected, result)
def _sequential_contents(seq_a, seq_b):
expected = (1, 2, 3, 4, 5, 6)
result = tuple(utils.chain_sorted(seq_a, seq_b))
assert_equal(expected, result)
def test_chain_sorted__single_sequence():
sequence = (1, 2, 3)
result = tuple(utils.chain_sorted(sequence))
assert_equal(sequence, result)
def test_chain_sorted__no_sequences():
expected = ()
result = tuple(utils.chain_sorted())
assert_equal(expected, result)
def test_chain_sorted__single_sequence():
sequence = (1, 2, 3)
result = tuple(utils.chain_sorted(sequence))
assert_equal(sequence, result)
def test_chain_sorted__invalid_keywords():
assert_raises(TypeError, tuple, utils.chain_sorted((1, 2, 3), foobar=None))
def test_chain_sorted__mixed_contents__reverse():
sequence_a = (-2, -3, -5)
sequence_b = (0, -1, -4)
expected = (0, -1, -2, -3, -4, -5)
result = tuple(utils.chain_sorted(sequence_a, sequence_b, reverse=True))
assert_equal(expected, result)
def _sequential_contents(seq_a, seq_b):
expected = (1, 2, 3, 4, 5, 6)
result = tuple(utils.chain_sorted(seq_a, seq_b))
assert_equal(expected, result)
def test_chain_sorted__invalid_keywords():
assert_raises(TypeError, tuple, utils.chain_sorted((1, 2, 3), foobar=None))
def test_chain_sorted__no_sequences():
expected = ()
result = tuple(utils.chain_sorted())
assert_equal(expected, result)
