def vcf_io(request):
io_config = {
"infile": relative_to_this_test_folder("fixtures/vcf_input.tsv"),
"outfile": "-",
}
io_config = FrozenBox(io_config)
io_manager = IOManager(io_config, IOType.TSV, IOType.TSV)
return io_manager
def variants_io_m(request):
io_config = FrozenBox({
"infile":
relative_to_this_test_folder("fixtures/input_multi.tsv"),
"outfile":
"-",
})
io_manager = IOManager(io_config, IOType.TSV, IOType.TSV)
return io_manager
def build(fixture_name, io_options=dict()):
io_config = {
"infile": relative_to_this_test_folder(fixture_name),
"outfile": "-",
}
io_options.update(io_config)
io_options = FrozenBox(io_options)
io_manager = IOManager(io_options, IOType.TSV, IOType.TSV)
return io_manager
def build(fixture_name, options=Box({})):
io_options = options.to_dict()
io_config = {
"infile": relative_to_this_test_folder(fixture_name),
"outfile": "-",
}
io_options.update(io_config)
io_options = Box(io_options, default_box=True, default_box_attr=None)
io_manager = IOManager(io_options, IOType.TSV, IOType.TSV)
return io_manager
def test_create_file_io():
io_config = FrozenBox({
"infile":
relative_to_this_test_folder("fixtures/input.tsv"),
"outfile":
"-",
})
with IOManager(io_config, IOType.TSV, IOType.TSV) as io:
assert io is not None
lines = list(io.lines_read_iterator())
print(lines)
assert len(lines) == 4
print(io.header)
assert len(io.header) == 3
def pipeline_main(argv):
gpf_instance = GPFInstance()
dae_config = gpf_instance.dae_config
genomes_db = gpf_instance.genomes_db
desc = "Program to annotate variants combining multiple annotating tools"
parser = argparse.ArgumentParser(
description=desc,
conflict_handler="resolve",
formatter_class=argparse.RawDescriptionHelpFormatter,
)
parser.add_argument('--verbose', '-V', action='count', default=0)
for name, args in main_cli_options(gpf_instance):
parser.add_argument(name, **args)
options = parser.parse_args()
if options.verbose == 1:
logging.basicConfig(level=logging.WARNING)
elif options.verbose == 2:
logging.basicConfig(level=logging.INFO)
elif options.verbose >= 3:
logging.basicConfig(level=logging.DEBUG)
else:
logging.basicConfig(level=logging.ERROR)
if options.annotation_config is not None:
config_filename = options.annotation_config
else:
config_filename = dae_config.annotation.conf_file
assert os.path.exists(config_filename), config_filename
options = Box(
{k: v
for k, v in options._get_kwargs()},
default_box=True,
default_box_attr=None,
)
# File IO format specification
reader_type = IOType.TSV
writer_type = IOType.TSV
if options.read_parquet:
reader_type = IOType.Parquet
if options.write_parquet:
writer_type = IOType.Parquet
start = time.time()
pipeline = PipelineAnnotator.build(
options,
config_filename,
genomes_db,
)
assert pipeline is not None
with IOManager(options, reader_type, writer_type) as io_manager:
pipeline.annotate_file(io_manager)
print("# PROCESSING DETAILS:", file=sys.stderr)
print("#", time.asctime(), file=sys.stderr)
print("#", " ".join(sys.argv[1:]), file=sys.stderr)
print(
"The program was running for [h:m:s]:",
str(datetime.timedelta(seconds=round(time.time() - start, 0))),
file=sys.stderr,
)
if options.tabix:
run_tabix(options.outfile)