remove helper functions get_bgcs_from_gcfs and get_strains_from_bgcs

src/nplinker/genomics/__init__.py

@@ -5,8 +5,6 @@
 from .utils import add_bgc_to_gcf
 from .utils import add_strain_to_bgc
 from .utils import generate_mappings_genome_id_bgc_id
-from .utils import get_bgcs_from_gcfs
-from .utils import get_strains_from_bgcs
 
 
 logging.getLogger(__name__).addHandler(logging.NullHandler())
@@ -16,8 +14,6 @@
     "BGC",
     "GCF",
     "generate_mappings_genome_id_bgc_id",
-    "get_bgcs_from_gcfs",
-    "get_strains_from_bgcs",
     "add_bgc_to_gcf",
     "add_strain_to_bgc",
 ]

src/nplinker/genomics/utils.py

@@ -158,22 +158,3 @@ def add_bgc_to_gcf(
         f"{len(gcf_missing_bgc)} GCF objects have missing BGC objects."
     )
     return gcf_with_bgc, gcf_without_bgc, gcf_missing_bgc
-
-
-def get_bgcs_from_gcfs(gcfs: list[GCF]) -> list[BGC]:
-    """Get all BGC objects from given GCF objects."""
-    s = set()
-    for gcf in gcfs:
-        s |= gcf.bgcs
-    return list(s)
-
-
-def get_strains_from_bgcs(bgcs: list[BGC]) -> StrainCollection:
-    """Get all strain objects from given BGC objects."""
-    sc = StrainCollection()
-    for bgc in bgcs:
-        if bgc.strain is not None:
-            sc.add(bgc.strain)
-        else:
-            logger.warning("Strain is None for BGC %s", bgc.bgc_id)
-    return sc

tests/genomics/test_utils.py

@@ -6,8 +6,6 @@
 from nplinker.genomics import add_bgc_to_gcf
 from nplinker.genomics import add_strain_to_bgc
 from nplinker.genomics import generate_mappings_genome_id_bgc_id
-from nplinker.genomics import get_bgcs_from_gcfs
-from nplinker.genomics import get_strains_from_bgcs
 from nplinker.globals import GENOME_BGC_MAPPINGS_FILENAME
 from nplinker.strain import Strain
 from nplinker.strain_collection import StrainCollection
@@ -156,21 +154,3 @@ def test_add_bgc_to_gcf_error(bgc_list, gcf_list_error):
     with pytest.raises(KeyError) as e:
         add_bgc_to_gcf(bgc_list, gcf_list_error)
     assert "BGC id 'BGC_04' from GCF object '1' not found" in e.value.args[0]
-
-
-def test_get_bgcs_from_gcfs(bgc_list, gcf_list):
-    """Test get_bgcs_from_gcfs function."""
-    add_bgc_to_gcf(bgc_list, gcf_list)
-    bgcs = get_bgcs_from_gcfs(gcf_list)
-    assert isinstance(bgcs, list)
-    assert len(bgcs) == 3
-    for i in bgcs:
-        assert isinstance(i, BGC)
-
-
-def test_get_strains_from_bgcs(strain_collection, bgc_list):
-    """Test get_strains_from_bgcs function."""
-    add_strain_to_bgc(strain_collection, bgc_list)
-    strains = get_strains_from_bgcs(bgc_list)
-    assert isinstance(strains, StrainCollection)
-    assert strains == strain_collection