def _check_there_will_be_output(module, args):
predicted_output = module.report_prediction(args)
if not predicted_output:
message = ("Executing the {} command with the input [{}] would not "
"create any output files. Review inputs and try again.")\
.format(args.subparser_name, args.input)
raise utils.UsageError(message)
def _check_input_readable(dummy, args):
try:
if os.path.isdir(args.input):
os.listdir(args.input)
else:
open(args.input, "r").close()
except (OSError, IOError):
raise utils.UsageError(("Specified input [{}] cannot be read. Review "
"inputs and try again.").format(args.input))
def _check_output_correct_type(module_name, output_path, required_type):
actual_type = _actual_type(output_path)
if required_type != actual_type:
raise utils.UsageError(("The {} command outputs a {}, but the "
"specified output [{}] is a {}. "
"Review inputs and try again.")\
.format(module_name,
required_type,
output_path,
actual_type))
def _create_temp_working_dir(dummy, args):
try:
_makepath(args.temp_working_dir)
if args.required_output_type == "directory":
_makepath(args.output)
except OSError:
parent_dir = os.path.dirname(args.temp_working_dir)
raise utils.UsageError(("Jacquard cannot write to output directory "
"[{}]. Review inputs and try again.")\
.format(parent_dir))
def _check_overwrite_existing_files(module, args):
output = args.output_path
if not os.path.isdir(output):
output = os.path.dirname(output)
existing_output_paths = sorted(glob.glob(os.path.join(output, "*")))
existing_output = set([os.path.basename(i) for i in existing_output_paths])
predicted_output = module.report_prediction(args)
collisions = sorted(list(existing_output.intersection(predicted_output)))
if collisions and not args.force:
message = _build_collision_message(args.subparser_name, collisions)
raise utils.UsageError(message)
def _check_input_correct_type(dummy, args):
module_name = args.subparser_name
input_path = args.input
required_type = args.required_input_type
actual_type = _actual_type(input_path)
if required_type != actual_type:
raise utils.UsageError(("The {} command requires a {} as "
"input, but the specified input [{}] is a {}. "
"Review inputs and try again.") \
.format(module_name,
required_type,
input_path,
actual_type))
def _get_format_tag_regex(args):
if args.tags and args.include_all:
msg = (
"Unable to process command-line arguments. --include_format_tags cannot "
"be specified if --include_all is specified.")
raise utils.UsageError(msg)
if args.include_all:
format_tag_regex = ['.*']
elif args.tags:
format_tag_regex = args.tags.split(",")
else:
format_tag_regex = _DEFAULT_INCLUDED_FORMAT_TAGS
return format_tag_regex
def _check_snp_indel_pairings(altered_file_names, args):
if not set([len(i) for i in altered_file_names.values()]) == set([1]):
if not args.allow_inconsistent_sample_sets:
error = 0
for file_names in altered_file_names.values():
if len(file_names) % 2 != 0:
message = ("File {} was missing a "
"corresponding snp/indel file.")
logger.error(message, file_names)
error = 1
if error:
message = ("Not all patients were represented by the same set "
"of caller-VCFs. Review inputs/command options to "
"align file pairings or use the flag "
"--allow_inconsistent_sample_sets.")
raise utils.UsageError(message)
def _validate_consistent_input(vcf_readers, include_all):
if not include_all:
untranslated_readers = []
translated = False
untranslated = False
for vcf_reader in vcf_readers:
if '##jacquard.translate.caller' in vcf_reader.metaheaders:
translated = True
else:
untranslated = True
untranslated_readers.append(vcf_reader)
if translated and untranslated:
msg = ("Some input VCFs [{}] were not translated by Jacquard. "
"Review input and/or use --included_all flag")\
.format(untranslated_readers)
raise utils.UsageError(msg)
def _check_input_exists(dummy, args):
if not os.path.exists(args.input):
raise utils.UsageError(("Specified input [{}] does not exist. Review "\
"inputs and try again.").format(args.input))