def test_compressed_output(self):
'It writes a gziped file'
in_fhand = self.make_fasta()
cat_bin = os.path.join(BIN_DIR, 'cat_seqs')
# bgzf does not work with STDOUT
try:
stderr = NamedTemporaryFile()
check_output([cat_bin, '-Z', in_fhand.name], stderr=stderr)
self.fail('CalledProcessError expected')
except CalledProcessError:
msg = 'bgzf is only available for seekable files'
assert msg in open(stderr.name).read()
# bgzf
out_fhand = NamedTemporaryFile()
check_output([cat_bin, '-Z', '-o', out_fhand.name, in_fhand.name])
result = GzipFile(out_fhand.name).read()
assert '\nACTATCATGGCAGATA\n' in result
# gzip
result = check_output([cat_bin, '-z', in_fhand.name])
result = GzipFile(fileobj=StringIO(result)).read()
assert '\nACTATCATGGCAGATA\n' in result
# bzip2
result = check_output([cat_bin, '-B', in_fhand.name])
result = BZ2File(StringIO(result)).read()
assert '\nACTATCATGGCAGATA\n' in result
def test_bzipped2_input(self):
# we need a compressed file
in_fhand = self.make_fasta()
cat_bin = os.path.join(BIN_DIR, 'cat_seqs')
out_fhand = NamedTemporaryFile()
check_output([cat_bin, '-B', '-o', out_fhand.name, in_fhand.name])
result = BZ2File(out_fhand.name).read()
assert '\nACTATCATGGCAGATA\n' in result
result = check_output([cat_bin, out_fhand.name])
assert '>seq1\nACTATCATGGCAGATA\n' in result
def uncompress_if_required(fhand):
'It returns a uncompressed handle if required'
magic = peek_chunk_from_file(fhand, 2)
if magic == '\037\213':
fhand = GzipFile(fileobj=fhand)
elif magic == 'BZ':
try:
fhand = BZ2File(fhand)
except NameError:
raise OptionalRequirementError(BZIP_ERROR)
return fhand
def compress_fhand(fhand, compression_kind=None):
'Compresses the file if required'
if compression_kind == BGZF:
if fhand_is_seekable(fhand):
fhand = BgzfWriter(fileobj=fhand)
else:
raise RuntimeError('bgzf is only available for seekable files')
elif compression_kind == GZIP:
fhand = GzipFile(fileobj=fhand)
elif compression_kind == BZIP2:
mode = 'w' if 'w' in fhand.mode else 'r'
try:
fhand = BZ2File(fhand, mode=mode)
except NameError:
raise OptionalRequirementError(BZIP_ERROR)
return fhand