def open_possibly_compressed_file(filename, compression_type=None):
""" Notionally, cast "filename" to a file-like object.
If filename is already file-like, return it.
If it's compressed, return a decompressing file-like object.
If it's a BAM file, return a file-like object that produces SAM format.
Otherwise, just return an open file!
"""
if hasattr(filename, 'read'):
return filename #It's already file-like
if compression_type is None:
compression_type = get_compression_type(filename)
if compression_type == 'none':
return open(filename, 'rb')
elif compression_type == 'gzip':
return gzip.open(filename, 'rb')
elif compression_type == 'bzip2':
return bz2.BZ2File(filename, 'rb')
elif compression_type == 'bam':
from nesoni import sam
return sam.open_bam(filename)
else:
raise grace.Error('Unknown compression type: '+compression_type)
def open_possibly_compressed_file(filename, compression_type=None):
""" Notionally, cast "filename" to a file-like object.
If filename is already file-like, return it.
If it's compressed, return a decompressing file-like object.
If it's a BAM file, return a file-like object that produces SAM format.
Otherwise, just return an open file!
"""
if hasattr(filename, 'read'):
return filename #It's already file-like
if compression_type is None:
compression_type = get_compression_type(filename)
if compression_type == 'none':
return open(filename, 'rb')
elif compression_type == 'gzip':
return gzip.open(filename, 'rb')
elif compression_type == 'bzip2':
return bz2.BZ2File(filename, 'rb')
elif compression_type == 'bam':
from nesoni import sam
return sam.open_bam(filename)
else:
raise grace.Error('Unknown compression type: ' + compression_type)
def open_possibly_compressed_file(filename):
""" Read a file. It might be compressed. """
#if isinstance(filename, file):
# return filename #Whatever
#peek, f = peek_and_pipe(open_possibly_remote_file(filename), 4)
from nesoni import sam
if sam.is_bam(filename):
return sam.open_bam(filename)
f = open(filename, 'rb')
peek = f.read(4)
f.close()
#f = open(filename,'rb')
if peek.startswith('\x1f\x8b'):
#command = 'gunzip'
return gzip.open(filename, 'rb')
elif peek.startswith('BZh'):
#command = 'bunzip2'
return bz2.BZFile(filename, 'rb')
else:
#command = None
return open(filename, 'rb')
def open_possibly_compressed_file(filename):
""" Read a file. It might be compressed. """
#if isinstance(filename, file):
# return filename #Whatever
#peek, f = peek_and_pipe(open_possibly_remote_file(filename), 4)
from nesoni import sam
if sam.is_bam(filename):
return sam.open_bam(filename)
f = open(filename,'rb')
peek = f.read(4)
f.close()
#f = open(filename,'rb')
if peek.startswith('\x1f\x8b'):
#command = 'gunzip'
return gzip.open(filename, 'rb')
elif peek.startswith('BZh'):
#command = 'bunzip2'
return bz2.BZFile(filename, 'rb')
else:
#command = None
return open(filename, 'rb')
