Commit 6e92ebde authored by Amandine  PERRIN's avatar Amandine PERRIN
Browse files

change taxid to test difference between genbank and refseq

parent 770b32a3
Pipeline #82240 failed with stages
in 6 minutes and 19 seconds
...@@ -693,8 +693,9 @@ def test_download_2taxid(caplog): ...@@ -693,8 +693,9 @@ def test_download_2taxid(caplog):
def test_download_refseq_vs_genbank(caplog): def test_download_refseq_vs_genbank(caplog):
""" """
Give a taxid of a subspecies, download strains from refseq, and then from genbank. Give a taxid of a subspecies, download strains from refseq, and then from genbank.
Currently, no strains in refseq, and 2 in genbank. Currently, no strains in refseq, and 8 in genbank.
39831 = Klebsiella pneumoniae subsp. rhinoscleromatis #39831 = Klebsiella pneumoniae subsp. rhinoscleromatis
60 = Vitreoscilla sp.
Later, there can be some in refseq, but always at least 2 more in genbank Later, there can be some in refseq, but always at least 2 more in genbank
""" """
caplog.set_level(logging.INFO) caplog.set_level(logging.INFO)
...@@ -702,7 +703,7 @@ def test_download_refseq_vs_genbank(caplog): ...@@ -702,7 +703,7 @@ def test_download_refseq_vs_genbank(caplog):
section = "refseq" section = "refseq"
NCBI_species = None NCBI_species = None
NCBI_species_taxid = "" NCBI_species_taxid = ""
NCBI_taxid = "39831" NCBI_taxid = "60"
NCBI_strains = "" NCBI_strains = ""
outdir = os.path.join(GENEPATH, "test_download_refseq_genbank") outdir = os.path.join(GENEPATH, "test_download_refseq_genbank")
levels = "" levels = ""
...@@ -721,7 +722,7 @@ def test_download_refseq_vs_genbank(caplog): ...@@ -721,7 +722,7 @@ def test_download_refseq_vs_genbank(caplog):
assert not os.path.isdir(ngd_outdir) assert not os.path.isdir(ngd_outdir)
# Check logs # Check logs
assert ("From refseq: Downloading genomes with NCBI_taxid = 39831") in caplog.text assert ("From refseq: Downloading genomes with NCBI_taxid = 60") in caplog.text
assert "ERROR" in caplog.text assert "ERROR" in caplog.text
assert ("No strain correspond to your request. If you are sure there should have " assert ("No strain correspond to your request. If you are sure there should have "
"some, check that you gave valid NCBI taxid and/or " "some, check that you gave valid NCBI taxid and/or "
...@@ -745,7 +746,7 @@ def test_download_refseq_vs_genbank(caplog): ...@@ -745,7 +746,7 @@ def test_download_refseq_vs_genbank(caplog):
assert os.path.isdir(db_dir) assert os.path.isdir(db_dir)
assert len(os.listdir(db_dir)) == nb_gen assert len(os.listdir(db_dir)) == nb_gen
# Check log giving only species taxid # Check log giving only species taxid
assert ("From genbank: Downloading genomes with NCBI_taxid = 39831") in caplog.text assert ("From genbank: Downloading genomes with NCBI_taxid = 60") in caplog.text
# Check that assembly summary file was donwloaded as expected # Check that assembly summary file was donwloaded as expected
sum_file = os.path.join(outdir2, "assembly_summary-refseq-genbank.txt" ) sum_file = os.path.join(outdir2, "assembly_summary-refseq-genbank.txt" )
assert os.path.isfile(sum_file) assert os.path.isfile(sum_file)
......
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