def test_autodownload_false(tmpdir):
collection = GenomeCollection(data_dir=str(tmpdir))
collection.autodownload = False
with pytest.raises(FileNotFoundError) as excinfo:
collection.get_taxid_infos("224308")
assert "No infos" in str(excinfo.value)
with pytest.raises(FileNotFoundError) as excinfo:
collection.get_taxid_genome_data_path("224308")
assert "No genome" in str(excinfo.value)
def test_delete_all_data_files(tmpdir):
collection = GenomeCollection(data_dir=str(tmpdir))
taxids = ["224308", "511145", "559292"]
for taxid in taxids:
collection.get_taxid_infos(taxid)
found_taxids = collection.list_locally_available_taxids("infos")
assert len(found_taxids) == 3
collection.remove_all_local_data_files()
found_taxids = collection.list_locally_available_taxids("infos")
assert len(found_taxids) == 0
def test_taxid_with_nonunique_genome(tmpdir):
taxid = 10710 # LAMBDA PHAGE - has 2 associated assemblies on NCBI
collection = GenomeCollection(data_dir=str(tmpdir))
with pytest.raises(OSError) as excinfo:
path = collection.get_taxid_infos(taxid)
assert "You will need to download" in str(excinfo.value)
collection.download_taxid_genome_infos_from_ncbi(taxid, assembly_id="#1")
path = collection.datafile_path(taxid, data_type="genomic_fasta")
assert not os.path.exists(path)
collection.get_taxid_genome_data_path(taxid)
assert os.path.exists(path)
def test_list_taxids(tmpdir):
collection = GenomeCollection(data_dir=str(tmpdir))
taxids = ["511145", "559292", PHAGE_TAXID]
found_taxids = collection.list_locally_available_taxids("infos")
assert len(found_taxids) == 0
for taxid in taxids:
collection.get_taxid_infos(taxid)
found_taxids = collection.list_locally_available_taxids("infos")
assert found_taxids == taxids
found_taxids = collection.list_locally_available_taxids("genomic_fasta")
assert len(found_taxids) == 0
collection.get_taxid_genome_data_path(PHAGE_TAXID)
found_taxids = collection.list_locally_available_taxids("genomic_fasta")
assert found_taxids == [PHAGE_TAXID]
found_taxids = collection.list_locally_available_taxids_names()
assert len(found_taxids) == 3
# For coverage!
collection.list_locally_available_taxids_names(print_mode=True)