def check_arguments(args):
errors = []
errors += check_inputs(args, stdin_allowed=True)
errors += check_outputs(args, stdout_allowed=True)
errors += check_cpu_count(args)
errors += check_file_arg(args.seqids_path, none_allowed=True,
prefix='-S/--seqids_path')
errors += check_file_arg(args.descriptions_path, none_allowed=True,
prefix='-D/--descriptions_path')
errors += check_file_arg(args.names_path, none_allowed=True,
prefix='-N/--names_path')
errors += check_file_arg(args.mol_types_path, none_allowed=True,
prefix='-M/--mol_types_path')
errors += check_file_arg(args.taxids_path, none_allowed=True,
prefix='-T/--taxids_path')
if args.input_format != 'genbank':
values = [args.names, args.mol_types, args.taxids]
paths = [args.names_path, args.mol_types_path, args.taxids_path]
prefixes = ['-n/-N', '-m/-M', '-t/-T']
for value, path, prefix in zip(values, paths, prefixes):
if value or path is not None:
errors += ('{}: These options require input file(s) '
'in GenBank format.'.format(prefix))
if args.comparison is None:
args.comparison = COMPARISON
if errors:
for error in errors:
print_stderr(error, prefix='ERROR')
sys.exit(1)
def check_arguments(args):
errors = []
errors += check_file_arg(args.input_path, stdio_allowed=True)
errors += check_file_arg(args.output_path,
mode='w',
stdio_allowed=True,
prefix='-o/--output_path')
if errors:
for error in errors:
print_stderr(error, prefix='ERROR')
sys.exit(1)
def check_arguments(args):
errors = []
errors += check_sequtils_inputs(args, stdin_allowed=True)
errors += check_file_arg(args.seq_counts_path,
mode='w',
none_allowed=True,
prefix='-S/--seq_counts_path')
errors += check_file_arg(args.base_counts_path,
mode='w',
none_allowed=True,
prefix='-C/--base_counts_path')
if errors:
for error in errors:
print_stderr(error, prefix='ERROR')
sys.exit(1)
def check_inputs(args,
ext=SEQFILE_EXTS,
zip_ext=ZIP_EXTS,
stdin_allowed=False):
errors = []
if args.input_paths is None:
args.input_paths = [STDIO_PATH]
try:
input_files_indexed = args.index_paths is not None
except AttributeError:
input_files_indexed = False
input_formats = set()
for input_path in args.input_paths:
error = check_file_arg(input_path,
ext=ext,
zip_ext=zip_ext,
stdio_allowed=stdin_allowed)
if error:
errors += error
else:
try:
input_format = check_seq_file_format(
input_path,
args.input_format,
default_format=SEQFILE_FORMAT,
file_indexed=input_files_indexed)
input_formats |= {input_format}
except ValueError as exc:
error = ['Input file ', input_path, ': ', str(exc)]
errors.append(''.join(error))
if (stdin_allowed and len(args.input_paths) > 1
and STDIO_PATH in args.input_paths):
errors.append('Standard input ({}) cannot be part of a list of '
'multiple input files.'.format(STDIO_PATH))
if len(input_formats) > 1:
errors.append('Input files must all have the same format.')
elif len(input_formats) == 1:
args.input_format = list(input_formats)[0]
if not input_files_indexed:
return errors
if len(args.index_paths) not in [1, len(args.input_paths)]:
errors.append('There must be one index file for each input file '
'or one for all.')
return errors
for index_path in args.index_paths:
errors += check_file_arg(index_path, prefix='-i/--index_paths')
return errors
def check_arguments(args):
errors = []
for annot_path in args.annot_paths:
errors += check_file_arg(annot_path, stdio_allowed=True)
errors += check_file_arg(args.tree_path, prefix='-t/--tree_path')
errors += check_file_arg(args.seqids_path,
none_allowed=True,
prefix='-s/--seqids_path')
errors += check_file_arg(args.output_path,
mode='w',
stdio_allowed=True,
prefix='-o/--output_path')
if errors:
for error in errors:
print_stderr(error, prefix='ERROR')
sys.exit(1)
def check_arguments(args):
errors = []
errors += check_inputs(args)
errors += check_outputs(args, stdout_allowed=True)
errors += check_cpu_count(args)
errors += check_file_arg(args.removed_path,
mode='w',
none_allowed=True,
prefix='-r/--removed')
if args.no_output:
args.output_paths = None
if errors:
for error in errors:
print_stderr(error, prefix='ERROR')
sys.exit(1)
def check_arguments(args):
errors = []
errors += check_inputs(args, zip_ext=BGZIP_EXT)
if args.output_path is None:
if len(args.input_paths) > 1:
args.output_path = 'index.idx'
else:
input_basename = os.path.basename(args.input_paths[0])
args.output_path = input_basename + '.idx'
errors += check_file_arg(args.output_path,
mode='w',
prefix='-o/--output_path')
if errors:
for error in errors:
print_stderr(error, prefix='ERROR')
sys.exit(1)
def check_outputs(args,
ext=SEQFILE_EXTS,
zip_ext=ZIP_EXTS,
stdout_allowed=False):
errors = []
if isinstance(args.output_path, list):
if args.output_path is None:
if not hasattr(args, 'no_output') or not args.no_output:
args.output_path = STDIO_PATH
output_paths = args.output_path
else:
if args.output_path is None:
if not hasattr(args, 'no_output') or not args.no_output:
args.output_path = [STDIO_PATH]
output_paths = [args.output_path]
try:
default_format = args.input_format
except AttributeError:
default_format = SEQFILE_FORMAT
output_formats = set()
for output_path in output_paths:
error = check_file_arg(output_path,
mode='w',
ext=ext,
zip_ext=zip_ext,
stdio_allowed=stdout_allowed,
prefix='-o/--output_path')
if error:
errors += error
else:
try:
output_format = check_seq_file_format(
output_path,
args.output_format,
default_format=default_format)
output_formats |= {output_format}
except ValueError as exc:
error = ['-o/--output_path: ', output_path, ': ', str(exc)]
errors.append(''.join(error))
if len(output_formats) > 1:
errors.append(prefix + ': Output files must all have the same format.')
elif len(output_formats) == 1:
args.output_format = list(output_formats)[0]
if stdout_allowed and len(output_paths) > 1 and STDIO_PATH in output_paths:
errors.append('Standard output ({}) cannot be part of a list of '
'multiple output files.'.format(STDIO_PATH))
try:
nb_inputs = len(args.input_paths)
except AttributeError:
return errors
try:
nb_indices = len(args.index_paths)
except (AttributeError, TypeError):
nb_indices = 0
if nb_inputs > 1 and nb_indices == 1 and len(output_paths) != 1:
errors.append('If a common index file is specified for all input '
'files, only one output file must be specified.')
elif len(output_paths) not in [1, nb_inputs]:
errors.append('There must be one output file for each input file '
'or one for all.')
return errors
def check_arguments(args):
errors = []
for annot_path in args.annot_paths:
errors += check_file_arg(annot_path, stdio_allowed=True)
for sample_path in args.sample_paths:
errors += check_file_arg(sample_path, prefix='-s/--sample_path')
errors += check_file_arg(args.tree_path, prefix='-t/--tree_path')
errors += check_file_arg(args.ref_path, prefix='-r/--ref_path')
errors += check_file_arg(args.info_path,
none_allowed=True,
prefix='-i/--info_path')
errors += check_dir_arg(args.output_dir_path,
mode='w',
create=True,
prefix='-o/--output_dir_path')
errors += check_bin_arg(args.lualatex_path, prefix='--lualatex_path')
errors += check_num_arg(args.min_level,
number_type=int,
mini=1,
prefix='-l/--min_level')
errors += check_num_arg(args.max_level,
number_type=int,
mini=1,
none_allowed=True,
prefix='-L/--max_level')
errors += check_num_arg(args.min_fold_change,
number_type=float,
mini=1.0,
prefix='-f/--min_fold_change')
errors += check_num_arg(args.max_pvalue,
number_type=float,
mini=0.0,
maxi=1.0,
prefix='-p/--max_pvalue')
errors += check_num_arg(args.min_seq_count,
number_type=int,
mini=0,
prefix='-n/--min_seq_count')
errors += check_num_arg(args.min_seq_prop,
number_type=float,
mini=0.0,
maxi=100.0,
prefix='-m/--min_seq_prop')
if args.max_level is not None and args.min_level > args.max_level:
error = '-l/-L: Max level must be greater than min level.'
errors.append(error)
if args.sample_names is not None:
if len(args.sample_names) != len(args.sample_paths):
error = ('-s/-S: The number of sample names does not match '
'the number of sample paths.')
errors.append(error)
if errors:
for error in errors:
print_stderr(error, prefix='ERROR')
sys.exit(1)
if args.output_types is None:
args.output_types = OUTPUT_TYPES
if not (args.process or args.function or args.component):
args.process, args.function, args.component = True, True, True
if not (args.up_reg or args.down_reg or args.not_reg):
args.up_reg, args.down_reg, args.not_reg = True, True, False