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 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 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
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
else:
try:
out_fhand = compress_fhand(out_fhand, compression_kind=comp_kind)
except RuntimeError, error:
parser.error(error)
# The default output format is the same as the first file
if in_format == GUESS_FORMAT:
if not guessed_in_format:
guessed_in_format = guess_format(wrapped_fhands[0])
out_format = guessed_in_format
else:
out_format = in_format
# The original fhands should be stored, because otherwise they would be
# closed
args = {'out_fhand': out_fhand, 'in_fhands': wrapped_fhands,
'out_format': out_format, 'original_in_fhands': in_fhands,
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
else:
try:
out_fhand = compress_fhand(out_fhand, compression_kind=comp_kind)
except RuntimeError, error:
parser.error(error)
# The default output format is the same as the first file
if in_format == GUESS_FORMAT:
if not guessed_in_format:
guessed_in_format = guess_format(wrapped_fhands[0])
out_format = guessed_in_format
else:
out_format = in_format
# The original fhands should be stored, because otherwise they would be
# closed
args = {
'out_fhand': out_fhand,
