def test_is_seekable(self):
"It tests wether the fhands are seekable or not"
# StringIO
fhand = StringIO("hola")
assert fhand_is_seekable(fhand)
# standard file
fhand = NamedTemporaryFile()
fhand.seek(0)
assert fhand_is_seekable(fhand)
# a wrapped BufferedReader
fhand2 = wrap_in_buffered_reader(fhand)
assert fhand_is_seekable(fhand2)
# pylint: disable=R0903
# pylint: disable=C0111
class NonSeekable(object):
"Just for testing"
pass
assert not fhand_is_seekable(NonSeekable())
class NonSeekable2(object):
def seek(self):
pass
def seekable(self):
return False
assert not fhand_is_seekable(NonSeekable2())
def test_is_seekable(self):
'It tests wether the fhands are seekable or not'
# StringIO
fhand = StringIO('hola')
assert fhand_is_seekable(fhand)
# standard file
fhand = NamedTemporaryFile()
fhand.seek(0)
assert fhand_is_seekable(fhand)
# a wrapped BufferedReader
fhand2 = wrap_in_buffered_reader(fhand)
assert fhand_is_seekable(fhand2)
# pylint: disable=R0903
# pylint: disable=C0111
class NonSeekable(object):
'Just for testing'
pass
assert not fhand_is_seekable(NonSeekable())
class NonSeekable2(object):
def seek(self):
pass
def seekable(self):
return False
assert not fhand_is_seekable(NonSeekable2())
def parse_basic_args(parser):
'It parses the command line and it returns a dict with the arguments.'
parsed_args = parser.parse_args()
# we have to wrap the file in a BufferedReader to allow peeking into stdin
wrapped_fhands = []
# if input is stdin it will be a fhand not a list of fhands.
# we have to convert to a list
in_fhands = parsed_args.input
if not isinstance(in_fhands, list):
in_fhands = [in_fhands]
for fhand in in_fhands:
fhand = wrap_in_buffered_reader(fhand)
fhand = uncompress_if_required(fhand)
wrapped_fhands.append(fhand)
in_format = parsed_args.in_format
out_fhand = getattr(parsed_args, OUTFILE)
comp_kind = get_requested_compression(parsed_args)
if isinstance(out_fhand, list):
new_out_fhands = []
for out_f in out_fhand:
try:
out_f = compress_fhand(out_f, compression_kind=comp_kind)
except RuntimeError, error:
print 'hello', error
parser.error(error)
new_out_fhands.append(out_f)
out_fhand = new_out_fhands
def test_io_open(self):
'It checks the file wrapping in ReaderBuffers'
# a standard file
fhand = NamedTemporaryFile()
fhand.write('hola')
fhand.flush()
fhand2 = open(fhand.name)
fhand3 = wrap_in_buffered_reader(fhand2, force_wrap=True)
assert fhand3.peek(10) == 'hola'
def test_io_open(self):
'It checks the file wrapping in ReaderBuffers'
# a standard file
fhand = NamedTemporaryFile()
fhand.write('hola')
fhand.flush()
fhand2 = open(fhand.name)
fhand3 = wrap_in_buffered_reader(fhand2, force_wrap=True)
assert fhand3.peek(10) == 'hola'
def parse_basic_args(parser):
'It parses the command line and it returns a dict with the arguments.'
parsed_args = parser.parse_args()
# we have to wrap the file in a BufferedReader to allow peeking into stdin
wrapped_fhands = []
# if input is stdin it will be a fhand not a list of fhands.
# we have to convert to a list
in_fhands = parsed_args.input
if not isinstance(in_fhands, list):
in_fhands = [in_fhands]
for fhand in in_fhands:
fhand = wrap_in_buffered_reader(fhand)
fhand = uncompress_if_required(fhand)
wrapped_fhands.append(fhand)
# We have to add the one_line to the fastq files in order to get the
# speed improvements of the seqitems
in_format = parsed_args.in_format
if in_format == GUESS_FORMAT:
for wrapped_fhand in wrapped_fhands:
get_format(wrapped_fhand)
else:
if in_format != get_format(wrapped_fhands[0]):
msg = 'The given input format does not correspond to the input'
msg += ' file'
raise WrongFormatError(msg)
if 'fastq' in in_format:
for wrapped_fhand in wrapped_fhands:
get_format(wrapped_fhand)
else:
# we dont set the first one because already did in the previous
# checking
for wrapped_fhand in wrapped_fhands[1:]:
set_format(wrapped_fhand, in_format)
out_fhand = getattr(parsed_args, OUTFILE)
comp_kind = get_requested_compression(parsed_args)
if isinstance(out_fhand, list):
new_out_fhands = []
for out_f in out_fhand:
try:
out_f = compress_fhand(out_f, compression_kind=comp_kind)
except RuntimeError, error:
parser.error(error)
new_out_fhands.append(out_f)
out_fhand = new_out_fhands
def get_input_fhand(in_fhand):
in_fhand = wrap_in_buffered_reader(in_fhand, buffering=DEF_FILE_BUFFER)
in_compressed = _vcf_is_gz(in_fhand)
if in_compressed and not _fhand_is_tellable(in_fhand):
msg = 'The given input has no tell member and it is compressed. '
msg += 'You cannot use gzip file through stdin, try to pipe it '
msg += 'uncompressed with zcat |'
raise RuntimeError(msg)
if in_compressed:
mod_in_fhand = gzip.GzipFile(fileobj=in_fhand)
else:
mod_in_fhand = in_fhand
return mod_in_fhand
def parse_basic_args(parser):
'It parses the command line and it returns a dict with the arguments.'
parsed_args = parser.parse_args()
# we have to wrap the file in a BufferedReader to allow peeking into stdin
wrapped_fhands = []
# if input is stdin it will be a fhand not a list of fhands.
# we have to convert to a list
in_fhands = parsed_args.input
if not isinstance(in_fhands, list):
in_fhands = [in_fhands]
for fhand in in_fhands:
fhand = wrap_in_buffered_reader(fhand)
fhand = uncompress_if_required(fhand)
wrapped_fhands.append(fhand)
# We have to add the one_line to the fastq files in order to get the
# speed improvements of the seqitems
in_format = parsed_args.in_format
if 'fastq' in in_format:
guessed_in_format = guess_format(wrapped_fhands[0])
if '-one_line' in guessed_in_format:
in_format += '-one_line'
else:
guessed_in_format = None
out_fhand = getattr(parsed_args, OUTFILE)
comp_kind = get_requested_compression(parsed_args)
if isinstance(out_fhand, list):
new_out_fhands = []
for out_f in out_fhand:
try:
out_f = compress_fhand(out_f, compression_kind=comp_kind)
except RuntimeError, error:
parser.error(error)
new_out_fhands.append(out_f)
out_fhand = new_out_fhands
def parse_basic_args(parser):
'It parses the command line and it returns a dict with the arguments.'
parsed_args = parser.parse_args()
# we have to wrap the file in a BufferedReader to allow peeking into stdin
wrapped_fhands = []
# if input is stdin it will be a fhand not a list of fhands.
# we have to convert to a list
in_fhands = parsed_args.input
if not isinstance(in_fhands, list):
in_fhands = [in_fhands]
for fhand in in_fhands:
fhand = wrap_in_buffered_reader(fhand)
fhand = uncompress_if_required(fhand)
wrapped_fhands.append(fhand)
# We have to add the one_line to the fastq files in order to get the
# speed improvements of the seqitems
in_format = parsed_args.in_format
if 'fastq' in in_format:
guessed_in_format = guess_format(wrapped_fhands[0])
if '-one_line' in guessed_in_format:
in_format += '-one_line'
else:
guessed_in_format = None
out_fhand = getattr(parsed_args, OUTFILE)
comp_kind = get_requested_compression(parsed_args)
if isinstance(out_fhand, list):
new_out_fhands = []
for out_f in out_fhand:
try:
out_f = compress_fhand(out_f, compression_kind=comp_kind)
except RuntimeError, error:
parser.error(error)
new_out_fhands.append(out_f)
out_fhand = new_out_fhands