diff --git a/src/ensembl_lite/_config.py b/src/ensembl_lite/_config.py index fc3d419..665efa4 100644 --- a/src/ensembl_lite/_config.py +++ b/src/ensembl_lite/_config.py @@ -27,6 +27,7 @@ class Config: species_dbs: dict[str, list[str]] align_names: Iterable[str] tree_names: Iterable[str] + homologies: bool def update_species(self, species: dict[str, list[str]]): if not species: @@ -210,7 +211,7 @@ def read_config(config_path) -> Config: install_path = ( pathlib.Path(parser.get("local path", "install_path")).expanduser().absolute() ) - + homologies = parser.has_option("compara", "homologies") species_dbs = {} get_option = parser.get align_names = [] @@ -248,4 +249,5 @@ def read_config(config_path) -> Config: species_dbs=species_dbs, align_names=align_names, tree_names=tree_names, + homologies=homologies, ) diff --git a/src/ensembl_lite/_download.py b/src/ensembl_lite/_download.py index b41d720..a5303bd 100644 --- a/src/ensembl_lite/_download.py +++ b/src/ensembl_lite/_download.py @@ -154,7 +154,7 @@ def __call__(self, name: str) -> bool: def download_homology(config: Config, debug: bool, verbose: bool): """downloads tsv homology files for each genome""" - if not any((config.align_names, config.tree_names)): + if not config.homologies: return site_map = get_site_map(config.host) diff --git a/src/ensembl_lite/data/sample.cfg b/src/ensembl_lite/data/sample.cfg index 052a69d..345cafa 100644 --- a/src/ensembl_lite/data/sample.cfg +++ b/src/ensembl_lite/data/sample.cfg @@ -13,4 +13,6 @@ db=core db=core [compara] align_names=10_primates.epo -tree_names=10_primates_EPO_default.nh \ No newline at end of file +tree_names=10_primates_EPO_default.nh +# if you want homology data, keep the following line +homologies =