def __init__(self, filename=None, mode="w", fileobj=None, compresslevel=6):
if fileobj:
assert filename is None
handle = fileobj
else:
if "w" not in mode.lower() and "a" not in mode.lower():
raise ValueError("Must use write or append mode, not %r" % mode)
if "a" in mode.lower():
handle = _open(filename, "ab")
else:
handle = _open(filename, "wb")
self._text = "b" not in mode.lower()
self._handle = handle
self._buffer = b""
self.compresslevel = compresslevel
def __init__(self, filename=None, mode="r", fileobj=None, max_cache=100):
# TODO - Assuming we can seek, check for 28 bytes EOF empty block
# and if missing warn about possible truncation (as in samtools)?
if max_cache < 1:
raise ValueError("Use max_cache with a minimum of 1")
# Must open the BGZF file in binary mode, but we may want to
# treat the contents as either text or binary (unicode or
# bytes under Python 3)
if fileobj:
assert filename is None
handle = fileobj
assert "b" in handle.mode.lower()
else:
if "w" in mode.lower() \
or "a" in mode.lower():
raise ValueError(
"Must use read mode (default), not write or append mode")
handle = _open(filename, "rb")
self._text = "b" not in mode.lower()
if self._text:
self._newline = "\n"
else:
self._newline = b"\n"
self._handle = handle
self.max_cache = max_cache
self._buffers = {}
self._block_start_offset = None
self._block_raw_length = None
self._load_block(handle.tell())
def __init__(self, filename=None, mode="r", fileobj=None, max_cache=100):
#TODO - Assuming we can seek, check for 28 bytes EOF empty block
#and if missing warn about possible truncation (as in samtools)?
if max_cache < 1:
raise ValueError("Use max_cache with a minimum of 1")
#Must open the BGZF file in binary mode, but we may want to
#treat the contents as either text or binary (unicode or
#bytes under Python 3)
if fileobj:
assert filename is None
handle = fileobj
assert "b" in handle.mode.lower()
else:
if "w" in mode.lower() \
or "a" in mode.lower():
raise ValueError("Must use read mode (default), not write or append mode")
handle = _open(filename, "rb")
self._text = "b" not in mode.lower()
if self._text:
self._newline = "\n"
else:
self._newline = b"\n"
self._handle = handle
self.max_cache = max_cache
self._buffers = {}
self._block_start_offset = None
self._block_raw_length = None
self._load_block(handle.tell())
def __init__(self, filename=None, mode="w", fileobj=None, compresslevel=6):
if fileobj:
assert filename is None
handle = fileobj
else:
if "w" not in mode.lower() \
and "a" not in mode.lower():
raise ValueError("Must use write or append mode, not %r" % mode)
if "a" in mode.lower():
handle = _open(filename, "ab")
else:
handle = _open(filename, "wb")
self._text = "b" not in mode.lower()
self._handle = handle
self._buffer = b""
self.compresslevel = compresslevel
def __init__(self, filename=None, mode="w", fileobj=None, compresslevel=6):
"""Initilize the class."""
if fileobj:
assert filename is None
handle = fileobj
else:
if "w" not in mode.lower() and "a" not in mode.lower():
raise ValueError("Must use write or append mode, not %r" %
mode)
if "a" in mode.lower():
raise NotImplementedError("Append mode is not implemented yet")
# handle = _open(filename, "ab")
else:
handle = _open(filename, "wb")
self._text = "b" not in mode.lower()
self._handle = handle
self._buffer = b""
self.compresslevel = compresslevel
