def test_append():
for ext in ["", ".gz"]: # BZ2 does NOT support append
text = "AB"
reference = text + text
filename = 'truncated.fastq' + ext
mode = 'a'
if ext != "":
mode = 'ab'
text = text.encode()
reference = text + text
text = get_compressor(filename).compress(
text) # On Py3, need to send BYTES, not unicode
print("Trying ext=%s" % ext)
with temporary_path(filename) as path:
try:
os.unlink(path)
except OSError:
pass
with open_output(path, mode) as f:
f.write(text)
print(path)
with open_output(path, mode) as f:
f.write(text)
with xopen(path, 'r') as f:
try:
reference = reference.decode("utf-8")
except AttributeError:
pass
for appended in f:
assert appended == reference
def test_truncated_gz_iter():
with raises(EOFError), temporary_path('truncated.gz') as path:
create_truncated_file(path)
f = xopen(path, 'r', use_system=False) # work around bug in py3.4
for line in f:
pass
f.close()
def get_writer(self, file_desc, compressed=False):
"""Create the writer for a file descriptor if it does not already
exist.
Args:
file_desc: File descriptor. If `compressed==True`, this is a tuple
(path, mode), otherwise it's only a path.
compressed: Whether data has already been compressed.
Returns:
The writer.
"""
if compressed:
path, mode = file_desc
else:
path = file_desc
if path not in self.writers:
if self.suffix:
real_path = add_suffix_to_path(path, self.suffix)
else:
real_path = path
# TODO: test whether O_NONBLOCK allows non-blocking write to NFS
if compressed:
self.writers[path] = open_output(real_path, mode)
else:
self.writers[path] = xopen(real_path, "w")
return self.writers[path]
def get_writer(self, file_desc, compressed=False):
"""Create the writer for a file descriptor if it does not already
exist.
Args:
file_desc: File descriptor. If `compressed==True`, this is a tuple
(path, mode), otherwise it's only a path.
compressed: Whether data has already been compressed.
Returns:
The writer.
"""
if compressed:
path, mode = file_desc
else:
path = file_desc
if path not in self.writers:
if self.suffix:
real_path = add_suffix_to_path(path, self.suffix)
else:
real_path = path
# TODO: test whether O_NONBLOCK allows non-blocking write to NFS
if compressed:
self.writers[path] = open_output(real_path, mode)
else:
self.writers[path] = xopen(real_path, "w")
return self.writers[path]
def test_append():
for ext in ["", ".gz"]: # BZ2 does NOT support append
text = "AB"
reference = text + text
filename = 'truncated.fastq' + ext
mode = 'a'
if ext != "":
mode = 'ab'
text = text.encode()
reference = text + text
text = get_compressor(filename).compress(text) # On Py3, need to send BYTES, not unicode
print("Trying ext=%s" % ext)
with temporary_path(filename) as path:
try:
os.unlink(path)
except OSError:
pass
with open_output(path, mode) as f:
f.write(text)
print(path)
with open_output(path, mode) as f:
f.write(text)
with xopen(path, 'r') as f:
try:
reference = reference.decode("utf-8")
except AttributeError:
pass
for appended in f:
assert appended == reference
def test_truncated_gz_iter():
with raises(EOFError), temporary_path('truncated.gz') as path:
create_truncated_file(path)
f = xopen(path, 'r', use_system=False) # work around bug in py3.4
for line in f:
pass
f.close()
def test_xopen_binary():
for name in files:
f = xopen(name, 'rb')
try:
lines = list(f)
assert len(lines) == 12
assert lines[5] == b'AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT\n', name
finally:
f.close()
def test_context_manager():
major, minor = sys.version_info[0:2]
for name in files:
if major == 2 and minor == 6:
continue # Py26 compression libraries do not support context manager protocol.
with xopen(name, 'rt') as f:
lines = list(f)
assert len(lines) == 12
assert lines[5] == 'AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT\n', name
def test_xopen_binary():
for name in files:
f = xopen(name, 'rb')
try:
lines = list(f)
assert len(lines) == 12
assert lines[5] == b'AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT\n', name
finally:
f.close()
def test_context_manager():
major, minor = sys.version_info[0:2]
for name in files:
if major == 2 and minor == 6:
continue # Py26 compression libraries do not support context manager protocol.
with xopen(name, 'rt') as f:
lines = list(f)
assert len(lines) == 12
assert lines[5] == 'AGCCGCTANGACGGGTTGGCCCTTAGACGTATCT\n', name
def create_truncated_file(path):
# Random text
text = ''.join(random.choice('ABCDEFGHIJKLMNOPQRSTUVWXYZ') for _ in range(200))
f = xopen(path, 'w')
f.write(text)
f.close()
f = open(path, 'a')
f.truncate(os.stat(path).st_size - 10)
f.close()
def create_truncated_file(path):
# Random text
text = ''.join(
random.choice('ABCDEFGHIJKLMNOPQRSTUVWXYZ') for _ in range(200))
f = xopen(path, 'w')
f.write(text)
f.close()
f = open(path, 'a')
f.truncate(os.stat(path).st_size - 10)
f.close()
def __init__(self, path, mode='r', quality_base=None, alphabet=None):
self.quality_base = quality_base
self.alphabet = alphabet
if isinstance(path, str):
self.name = path
self._file = xopen(path, mode)
self._close_on_exit = True
else:
if hasattr(path, 'name'):
self.name = path.name
else:
# TODO: generate random unique name?
self.name = path.__class__
self._file = path
def __init__(self, path, mode='r', quality_base=None, alphabet=None):
self.quality_base = quality_base
self.alphabet = alphabet
if isinstance(path, str):
self.name = path
self._file = xopen(path, mode)
self._close_on_exit = True
else:
if hasattr(path, 'name'):
self.name = path.name
else:
# TODO: generate random unique name?
self.name = path.__class__
self._file = path
def __init__(
self, path, quality_base=33, sequence_class=Sequence,
alphabet=None):
self._close_on_exit = False
if isinstance(path, str):
path = xopen(path, 'rb')
self._close_on_exit = True
if isinstance(path, str):
self.name = path
else:
self.name = path.name
self._file = path
self.quality_base = quality_base
self.sequence_class = sequence_class
self.alphabet = alphabet
def __init__(self,
path,
quality_base=33,
sequence_class=Sequence,
alphabet=None):
self._close_on_exit = False
if isinstance(path, str):
path = xopen(path, 'rb')
self._close_on_exit = True
if isinstance(path, str):
self.name = path
else:
self.name = path.name
self._file = path
self.quality_base = quality_base
self.sequence_class = sequence_class
self.alphabet = alphabet
def test_truncated_gz():
with raises(EOFError), temporary_path('truncated.gz') as path:
create_truncated_file(path)
f = xopen(path, 'r')
f.read()
f.close()
def test_truncated_gz():
with raises(EOFError), temporary_path('truncated.gz') as path:
create_truncated_file(path)
f = xopen(path, 'r')
f.read()
f.close()
