def test_binaries(self):
'It test the binaries'
interleave_bin = os.path.join(BIN_DIR, 'interleave_pairs')
deinterleave_bin = os.path.join(BIN_DIR, 'deinterleave_pairs')
assert 'usage' in check_output([interleave_bin, '-h'])
assert 'usage' in check_output([deinterleave_bin, '-h'])
in_fpath1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
in_fpath2 = os.path.join(TEST_DATA_DIR, 'pairend1b.sfastq')
out_fhand = NamedTemporaryFile()
check_output(
[interleave_bin, '-o', out_fhand.name, in_fpath1, in_fpath2])
result = open(out_fhand.name).read()
assert '@seq5:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in result
assert '@seq5:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in result
out_fhand1 = NamedTemporaryFile()
out_fhand2 = NamedTemporaryFile()
check_output([
deinterleave_bin, '-o', out_fhand1.name, out_fhand2.name,
out_fhand.name
])
assert open(in_fpath1).read() == open(out_fhand1.name).read()
assert open(in_fpath2).read() == open(out_fhand2.name).read()
out_fhand1 = NamedTemporaryFile()
out_fhand2 = NamedTemporaryFile()
check_output([
deinterleave_bin, '-o', out_fhand1.name, out_fhand2.name,
out_fhand.name, '-Z'
])
assert open(in_fpath1).read() == BgzfReader(out_fhand1.name).read(2000)
assert open(in_fpath2).read() == BgzfReader(out_fhand2.name).read(2000)
# skip checks
in_fpath1 = os.path.join(TEST_DATA_DIR, 'pairend1.sfastq')
in_fpath2 = os.path.join(TEST_DATA_DIR, 'pairend2.sfastq')
out_fhand = NamedTemporaryFile()
stderr = NamedTemporaryFile()
ret_code = call(
[interleave_bin, '-o', out_fhand.name, in_fpath1, in_fpath2],
stderr=stderr)
assert int(ret_code)
assert 'from the two files do not match' in open(stderr.name).read()
check_output(
[interleave_bin, '-o', out_fhand.name, '-s', in_fpath1, in_fpath2])
result = open(out_fhand.name).read()
assert 'seq4:136:FC706VJ:2:2104:15343:197393' in result
assert 'seq3:136:FC706VJ:2:2104:15343:197393' in result
def test_pair_matcher_bin(self):
'It test the pair matcher binary'
pair_matcher_bin = os.path.join(SEQ_BIN_DIR, 'pair_matcher')
assert 'usage' in check_output([pair_matcher_bin, '-h'])
in_fpath = os.path.join(TEST_DATA_DIR, 'pairend5.sfastq')
out_fhand = NamedTemporaryFile()
orphan_fhand = NamedTemporaryFile()
check_output([
pair_matcher_bin, '-o', out_fhand.name, '-p', orphan_fhand.name,
in_fpath
])
result = open(out_fhand.name).read()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in result
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in result
orp = open(orphan_fhand.name).read()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# compressed output
in_fpath = os.path.join(TEST_DATA_DIR, 'pairend5.sfastq')
out_fhand = NamedTemporaryFile()
orphan_fhand = NamedTemporaryFile()
check_output([
pair_matcher_bin, '-o', out_fhand.name, '-p', orphan_fhand.name,
in_fpath, '-Z'
])
result = BgzfReader(out_fhand.name).read(2000)
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in result
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in result
orp = BgzfReader(orphan_fhand.name).read(2000)
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# unordered file
in_fpath = os.path.join(TEST_DATA_DIR, 'pairend6.sfastq')
out_fhand = NamedTemporaryFile()
orphan_fhand = NamedTemporaryFile()
check_output([
pair_matcher_bin, '-o', out_fhand.name, '-p', orphan_fhand.name,
in_fpath, '-u'
])
result = open(out_fhand.name).read()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in result
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in result
orp = open(orphan_fhand.name).read()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
def __init__(self, pbiFilename, chunk_size=10000000):
self._chunk_start = None
self._pbiFilename = abspath(expanduser(pbiFilename))
self._get_blocks()
with BgzfReader(self._pbiFilename, mode='rb') as f:
self._loadHeader(f)
holeNumbers = self._loadMainIndex(f,
self._to_virtual_offset,
zmw_only=True)
self._make_chunks(chunk_size, holeNumbers)
def __init__(self,
pbiFilename,
chunk_start=None,
chunk_size=None,
to_virtual_offset=None):
self._chunk_start = chunk_start
self._chunk_size = chunk_size
pbiFilename = abspath(expanduser(pbiFilename))
with BgzfReader(pbiFilename, mode='rb') as f:
self._loadHeader(f)
self._loadMainIndex(f, to_virtual_offset)
self._loadOffsets(f)
def test_pair_matcher_bin(self):
'It test the pair matcher binary'
pair_matcher_bin = os.path.join(BIN_DIR, 'pair_matcher')
assert 'usage' in check_output([pair_matcher_bin, '-h'])
in_fpath = os.path.join(TEST_DATA_DIR, 'pairend5.sfastq')
out_fhand = NamedTemporaryFile()
orphan_fhand = NamedTemporaryFile()
check_output([
pair_matcher_bin, '-o', out_fhand.name, '-p', orphan_fhand.name,
in_fpath
])
result = open(out_fhand.name).read()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in result
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in result
orp = open(orphan_fhand.name).read()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
in_fpath = os.path.join(TEST_DATA_DIR, 'pairend5.sfastq')
out_fhand = NamedTemporaryFile()
orphan_fhand = NamedTemporaryFile()
stderr = NamedTemporaryFile()
try:
check_output([
pair_matcher_bin, '-o', out_fhand.name, '-p',
orphan_fhand.name, in_fpath, '-l', '1'
],
stderr=stderr)
self.fail('error expected')
except CalledProcessError:
assert 'There are too many consecutive' in open(stderr.name).read()
# compressed output
in_fpath = os.path.join(TEST_DATA_DIR, 'pairend5.sfastq')
out_fhand = NamedTemporaryFile()
orphan_fhand = NamedTemporaryFile()
check_output([
pair_matcher_bin, '-o', out_fhand.name, '-p', orphan_fhand.name,
in_fpath, '-Z'
])
result = BgzfReader(out_fhand.name).read(2000)
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in result
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in result
orp = BgzfReader(orphan_fhand.name).read(2000)
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
# unordered file
in_fpath = os.path.join(TEST_DATA_DIR, 'pairend6.sfastq')
out_fhand = NamedTemporaryFile()
orphan_fhand = NamedTemporaryFile()
check_output([
pair_matcher_bin, '-o', out_fhand.name, '-p', orphan_fhand.name,
in_fpath, '-u'
])
result = open(out_fhand.name).read()
assert '@seq1:136:FC706VJ:2:2104:15343:197393 1:Y:18:ATCACG' in result
assert '@seq1:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in result
orp = open(orphan_fhand.name).read()
assert '@seq8:136:FC706VJ:2:2104:15343:197393 2:Y:18:ATCACG' in orp
def __init__(self, pbiFilename):
pbiFilename = abspath(expanduser(pbiFilename))
with BgzfReader(pbiFilename, mode='rb') as f:
self._loadHeader(f)