module plugins.sample_processors.genomepy

Fetch genome resources with mod:genomepy.

---

class SampleProcessorGenomePy

Fetch genome resources with mod:genomepy.

Args:

• records: Pandas DataFrame object.
• config: Config object.

Attributes:

• records: Pandas DataFrame object.
• config: Config object.

---

method fetch_resources

fetch_resources(genomes_dir_root: Path) → Dict[str, Tuple[Path, Path]]

Fetch assemblies.

Args:

• genomes_dir_root: Path to fetch assemblies to.

Returns: Dictionary with genome resource paths.

---

method process

process(
    loc: Path = PosixPath('/home/runner/work/zarp-cli/zarp-cli')
) → DataFrame

Fetch genome resources with mod:genomepy.

Args:

• loc: Path to fetch resources to. Resources may be located within child directories. Defaults to current working directory.

Returns: Dataframe with local path information for genome resources.

---

method set_assemblies

set_assemblies() → None

Set assemblies.

---

method set_resource_paths

set_resource_paths(resource_paths: Dict[str, Tuple[Path, Path]]) → None

Set resource paths.

Args:

• resource_paths: Dictionary with genome resource paths.