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# cython: language_level=3
"""Functions that read and write block gzipped files.
The user of the file doesn't have to worry about the compression
and random access is allowed if an index file is present."""
# based on Python 3.5's gzip module
import io
from libc.stdint cimport int8_t, int16_t, int32_t, int64_t
from libc.stdint cimport uint8_t, uint16_t, uint32_t, uint64_t
from libc.stdio cimport SEEK_SET
from libc.stdlib cimport malloc, calloc, realloc, free
from cpython.object cimport PyObject
from cpython.bytes cimport PyBytes_FromStringAndSize, _PyBytes_Resize
from pysam.libcutils cimport force_bytes, encode_filename
from pysam.libchtslib cimport bgzf_open, bgzf_index_build_init, bgzf_write, bgzf_read, \
bgzf_flush, bgzf_index_dump, bgzf_close, bgzf_seek, \
bgzf_tell, bgzf_getline, kstring_t, BGZF
__all__ = ["BGZFile"]
BUFFER_SIZE = io.DEFAULT_BUFFER_SIZE
cdef class BGZFile(object):
"""The BGZFile class simulates most of the methods of a file object with
the exception of the truncate() method.
This class only supports opening files in binary mode. If you need to open a
compressed file in text mode, use the gzip.open() function.
"""
cdef BGZF* bgzf
cdef readonly object name, index
def __init__(self, filename, mode=None, index=None):
"""Constructor for the BGZFile class.
The mode argument can be any of 'r', 'rb', 'a', 'ab', 'w', 'wb', 'x', or
'xb' depending on whether the file will be read or written. The default
is the mode of fileobj if discernible; otherwise, the default is 'rb'.
A mode of 'r' is equivalent to one of 'rb', and similarly for 'w' and
'wb', 'a' and 'ab', and 'x' and 'xb'.
"""
if mode and ('t' in mode or 'U' in mode):
raise ValueError("Invalid mode: {!r}".format(mode))
if not mode:
mode = 'rb'
elif mode and 'b' not in mode:
mode += 'b'
mode = force_bytes(mode)
self.name = encode_filename(filename)
self.index = encode_filename(index) if index is not None else None
self.bgzf = bgzf_open(self.name, mode)
if self.bgzf.is_write and index is not None and bgzf_index_build_init(self.bgzf) < 0:
raise IOError('Error building bgzf index')
def __dealloc__(self):
self.close()
def write(self, data):
if not self.bgzf:
raise ValueError("write() on closed BGZFile object")
if not self.bgzf.is_write:
import errno
raise IOError(errno.EBADF, "write() on read-only BGZFile object")
if isinstance(data, bytes):
length = len(data)
else:
# accept any data that supports the buffer protocol
data = memoryview(data)
length = data.nbytes
if length > 0 and bgzf_write(self.bgzf, <char *>data, length) < 0:
raise IOError('BGZFile write failed')
return length
def read(self, size=-1):
cdef ssize_t read_size
if not self.bgzf:
raise ValueError("read() on closed BGZFile object")
if self.bgzf.is_write:
import errno
raise IOError(errno.EBADF, "read() on write-only BGZFile object")
if size < 0:
chunks = []
while 1:
chunk = PyBytes_FromStringAndSize(NULL, BUFFER_SIZE)
cdata = <bytes>chunk
read_size = bgzf_read(self.bgzf, <char *>chunk, BUFFER_SIZE)
if read_size < 0:
raise IOError('Error reading from BGZFile')
elif not read_size:
break
elif read_size < BUFFER_SIZE:
chunk = chunk[:read_size]
chunks.append(chunk)
return b''.join(chunks)
elif size > 0:
chunk = PyBytes_FromStringAndSize(NULL, size)
read_size = bgzf_read(self.bgzf, <char *>chunk, size)
if read_size < 0:
raise IOError('Error reading from BGZFile')
elif read_size < size:
chunk = chunk[:read_size]
return chunk
else:
return b''
@property
def closed(self):
return self.bgzf == NULL
def close(self):
if not self.bgzf:
return
if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0:
raise IOError('Error flushing BGZFile object')
if self.index and bgzf_index_dump(self.bgzf, self.index, NULL) < 0:
raise IOError('Cannot write index')
cdef ret = bgzf_close(self.bgzf)
self.bgzf = NULL
if ret < 0:
raise IOError('Error closing BGZFile object')
def __enter__(self):
return self
def __exit__(self, type, value, tb):
self.close()
def flush(self):
if not self.bgzf:
return
if self.bgzf.is_write and bgzf_flush(self.bgzf) < 0:
raise IOError('Error flushing BGZFile object')
def fileno(self):
"""Invoke the underlying file object's fileno() method.
This will raise AttributeError if the underlying file object
doesn't support fileno().
"""
raise AttributeError('fileno')
def rewind(self):
'''Return the uncompressed stream file position indicator to the
beginning of the file'''
if not self.bgzf:
raise ValueError("rewind() on closed BGZFile object")
if not self.bgzf.is_write:
raise IOError("Can't rewind in write mode")
if bgzf_seek(self.bgzf, 0, SEEK_SET) < 0:
raise IOError('Error seeking BGZFFile object')
def readable(self):
if not self.bgzf:
raise ValueError("readable() on closed BGZFile object")
return self.bgzf != NULL and not self.bgzf.is_write
def writable(self):
return self.bgzf != NULL and self.bgzf.is_write
def seekable(self):
return True
def tell(self):
if not self.bgzf:
raise ValueError("seek() on closed BGZFile object")
cdef int64_t off = bgzf_tell(self.bgzf)
if off < 0:
raise IOError('Error in tell on BGZFFile object')
return off
def seek(self, offset, whence=io.SEEK_SET):
if not self.bgzf:
raise ValueError("seek() on closed BGZFile object")
if whence is not io.SEEK_SET:
raise ValueError('Seek from end not supported')
cdef int64_t off = bgzf_seek(self.bgzf, offset, SEEK_SET)
if off < 0:
raise IOError('Error seeking BGZFFile object')
return off
def readline(self, size=-1):
if not self.bgzf:
raise ValueError("readline() on closed BGZFile object")
cdef kstring_t line
cdef char c
line.l = line.m = 0
line.s = NULL
cdef int ret = bgzf_getline(self.bgzf, b'\n', &line)
if ret == -1:
s = b''
elif ret == -2:
if line.m:
free(line.s)
raise IOError('Error reading line in BGZFFile object')
else:
s = line.s[:line.l]
if line.m:
free(line.s)
return s
def __iter__(self):
return self
def __next__(self):
line = self.readline()
if not line:
raise StopIteration()
return line
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