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use mocking for C. blochmannia kraken tests
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@widdowquinn
widdowquinn committed Feb 20, 2024
1 parent 86231a6 commit c7ed5e2
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6 changes: 5 additions & 1 deletion pyani/scripts/subcommands/subcmd_download.py
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Original file line number Diff line number Diff line change
Expand Up @@ -196,7 +196,11 @@ def extract_genomes(args: Namespace, dlstatus: download.DLStatus, esummary) -> N

# Modify sequence ID header if Kraken option active
if args.kraken:
logger.warning("Modifying downloaded sequence for Kraken compatibility")
logger.warning(
termcolor(
"Modifying downloaded sequence for Kraken compatibility", "magenta"
)
)
seqdata = list(SeqIO.parse(ename, "fasta"))
logger.debug("Modifying %s", ename)
for seq in seqdata:
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232 changes: 232 additions & 0 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -656,6 +656,238 @@ def mock_genome_hash(*args, **kwargs):
monkeypatch.setattr(download, "retrieve_genome_and_hash", mock_genome_hash)


@pytest.fixture
def mock_blochmannia_kraken_dl(monkeypatch):
"""Mocks remote database calls for multi-genome download.
Masks calls to the download module, for safe testing. This
fixture is used for Kraken-compatible file downloads
"""

def mock_asmuids(*args, **kwargs):
"""Mock download.get_asm_uids()."""
return ASMIDs(
"txid203804[Organism:exp]",
9,
[
"12545401", # GCF_023016305.1
"8228891", # GCF_014857065.1
"5431901", # GCF_009827135.1
"522068", # GCF_000331065.1
"444958", # GCF_000185985.2
"322791", # GCF_000973545.1
"322771", # GCF_000973505.1
"275848", # GCF_000185985.1
"61868", # GCF_000043285.1
"32848", # GCF_000011745.1
],
)

def mock_ncbi_esummary(*args, **kwargs):
"""Mock download.get_ncbi_esummary()
As this is a multi-genome download, the function needs to respond to
a passed argument, which is the assembly UID.
"""
data = {
"12545401": (
{
"Taxid": "101534",
"SpeciesTaxid": "101534",
"AssemblyAccession": "GCF_023016305.1",
"AssemblyName": "ASM230160v1",
"SpeciesName": "Candidatus Blochmannia pennsylvanicus",
},
"GCF_023016305.1_ASM2301630v1",
),
"8228891": (
{
"Taxid": "2681987",
"SpeciesTaxid": "2681987",
"AssemblyAccession": "GCF_014857065.1",
"AssemblyName": "ASM1485706v1",
"SpeciesName": "Blochmannia endosymbiont of Colobopsis nipponica",
},
"GCF_014857065.1_ASM1485706v1",
),
"5431901": (
{
"Taxid": "2681986",
"SpeciesTaxid": "2681986",
"AssemblyAccession": "GCF_009827135.1",
"AssemblyName": "ASM982713v1",
"SpeciesName": "Blochmannia endosymbiont of Camponotus nipponensis",
},
"GCF_009827135.1_ASM982713v1",
),
"522068": (
{
"Taxid": "1240471",
"SpeciesTaxid": "1240471",
"AssemblyAccession": "GCF_000331065.1",
"AssemblyName": "ASM33106v1",
"SpeciesName": "Candidatus Blochmannia chromaiodes",
},
"GCF_000331065.1_ASM33106v1",
),
"444958": (
{
"Taxid": "859654",
"SpeciesTaxid": "859654",
"AssemblyAccession": "GCF_000185985.2",
"AssemblyName": "ASM18598v2",
"SpeciesName": "Candidatus Blochmannia vafer",
},
"GCF_000185985.2_ASM18598v2",
),
"322791": (
{
"Taxid": "1505597",
"SpeciesTaxid": "1505597",
"AssemblyAccession": "GCF_000973545.1",
"AssemblyName": "ASM97354v1",
"SpeciesName": "Blochmannia endosymbiont of Camponotus (Colobopsis) obliquus",
},
"GCF_000973545.1_ASM97354v1",
),
"322771": (
{
"Taxid": "1505596",
"SpeciesTaxid": "1505596",
"AssemblyAccession": "GCF_000973505.1",
"AssemblyName": "ASM97350v1",
"SpeciesName": "Blochmannia endosymbiont of Polyrhachis (Hedomyrma) turneri",
},
"GCF_000973505.1_ASM97350v1",
),
"275848": (
{
"Taxid": "859654",
"SpeciesTaxid": "251535",
"AssemblyAccession": "GCF_000185985.2",
"AssemblyName": "ASM18598v2",
"SpeciesName": "Candidatus Blochmannia vafer",
},
"GCF_000185985.2_ASM18598v2",
),
"61868": (
{
"Taxid": "203907",
"SpeciesTaxid": "203907",
"AssemblyAccession": "GCF_000043285.1",
"AssemblyName": "ASM4328v1",
"SpeciesName": "Candidatus Blochmannia floridanus",
},
"GCF_000043285.1_ASM4328v1",
),
"32848": (
{
"Taxid": "291272",
"SpeciesTaxid": "101534",
"AssemblyAccession": "GCF_000011745.1",
"AssemblyName": "ASM1174v1",
"SpeciesName": "Candidatus Blochmannia floridanus",
},
"GCF_000011745.1_ASM1174v1",
),
}

return data[args[0]]

genomedir = FIXTUREPATH / "C_blochmannia_kraken"

def mock_genome_hash(*args, **kwargs):
"""Mock download.retrieve_genome_and_hash()."""
data = {
"GCF_023016305.1_ASM2301630v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_023016305.1_ASM2301630v1_genomic.fna.gz",
genomedir / "GCF_023016305.1_ASM2301630v1_hashes.txt",
False,
None,
),
"GCF_014857065.1_ASM1485706v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_014857065.1_ASM1485706v1_genomic.fna.gz",
genomedir / "GCF_014857065.1_ASM1485706v1_hashes.txt",
False,
None,
),
"GCF_009827135.1_ASM982713v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_009827135.1_ASM982713v1_genomic.fna.gz",
genomedir / "GCF_009827135.1_ASM982713v1_hashes.txt",
False,
None,
),
"GCF_000331065.1_ASM33106v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_000331065.1_ASM33106v1_genomic.fna.gz",
genomedir / "GCF_000331065.1_ASM33106v1_hashes.txt",
False,
None,
),
"GCF_000185985.2_ASM18598v2": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_000185985.2_ASM18598v2_genomic.fna.gz",
genomedir / "GCF_000185985.2_ASM18598v2_hashes.txt",
False,
None,
),
"GCF_000973545.1_ASM97354v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_000973545.1_ASM97354v1_genomic.fna.gz",
genomedir / "GCF_000973545.1_ASM97354v1_hashes.txt",
False,
None,
),
"GCF_000973505.1_ASM97350v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_000973505.1_ASM97350v1_genomic.fna.gz",
genomedir / "GCF_000973505.1_ASM97350v1_hashes.txt",
False,
None,
),
"GCF_000185985.1_ASM18598v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_000185985.1_ASM18598v1_genomic.fna.gz",
genomedir / "GCF_000185985.1_ASM18598v1_hashes.txt",
False,
None,
),
"GCF_000043285.1_ASM4328v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_000043285.1_ASM4328v1_genomic.fna.gz",
genomedir / "GCF_000043285.1_ASM4328v1_hashes.txt",
False,
None,
),
"GCF_000011745.1_ASM1174v1": DLStatus(
"ftp://ftp.ncbi.nlm.nih.gov/dummy_genomic.fna.gz",
"ftp://ftp.ncbi.nlm.nih.gov/dummy/md5checksums.txt",
genomedir / "GCF_000011745.1_ASM1174v1_genomic.fna.gz",
genomedir / "GCF_000011745.1_ASM1174v1_hashes.txt",
False,
None,
),
}

return data[args[0]]

monkeypatch.setattr(download, "get_asm_uids", mock_asmuids)
monkeypatch.setattr(download, "get_ncbi_esummary", mock_ncbi_esummary)
monkeypatch.setattr(download, "retrieve_genome_and_hash", mock_genome_hash)


@pytest.fixture
def nucmer_available():
"""Test that nucmer is available."""
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2 changes: 1 addition & 1 deletion tests/test_subcmd_01_download.py
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Original file line number Diff line number Diff line change
Expand Up @@ -138,6 +138,6 @@ def test_download_c_blochmannia(base_download_namespace, mock_blochmannia_dl):
subcommands.subcmd_download(base_download_namespace)


def test_download_kraken(kraken_namespace):
def test_download_kraken(kraken_namespace, mock_blochmannia_kraken_dl):
"""C. blochmannia download in Kraken format."""
subcommands.subcmd_download(kraken_namespace)

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