def test_GenomeGroup_covered_targets(filter_codes, binop_file, mock_binop_coverage_file):
"""Mock coverage file sets lines 6 and 10 (not 15) to be covered."""
ggrp = GenomeGroup(binop_file)
ggrp.set_coverage(mock_binop_coverage_file)
ggrp.set_filter(filter_codes)
assert len(ggrp.targets) == 4
assert len(ggrp.covered_targets) == 3
for ct in ggrp.covered_targets:
assert ct.source_path == binop_file
assert ct.loc_idx.lineno in [6, 10]
diff = list(ggrp.targets - ggrp.covered_targets)
assert diff[0].loc_idx.lineno == 15
def get_genome_group(src_loc: Path, config: Config) -> GenomeGroup:
"""Get the ``GenomeGroup`` based on ``src_loc`` and ``config``.
``Config`` is used to set global filter codes and exclude files on group creation.
Args:
src_loc: Path, can be directory or file
config: the running config object
Returns:
``GenomeGroup`` based on ``src_loc`` and config.
"""
ggrp = GenomeGroup()
# check if src_loc is a single file, otherwise assume it's a directory
if src_loc.is_file():
ggrp.add_file(source_file=src_loc)
else:
ggrp.add_folder(source_folder=src_loc,
exclude_files=config.exclude_files,
ignore_test_files=True)
if config.filter_codes:
LOGGER.info("Category restriction, chosen categories: %s",
sorted(config.filter_codes))
ggrp.set_filter(filter_codes=config.filter_codes)
for k, genome in ggrp.items():
LOGGER.info(
"%s",
colorize_output(
f"{len(genome.targets)} mutation targets found in {genome.source_file} AST.",
"green" if len(genome.targets) > 0 else "yellow",
),
)
for e in config.exclude_files:
LOGGER.info("%s", colorize_output(f"{e.resolve()} excluded.",
"yellow"))
return ggrp
