diff --git a/test/test_functional/test_prepare.py b/test/test_functional/test_prepare.py
index 4a84da725e45cc45dea21e0b0ddbaeccc2dd5f06..d04ee928aa32d3c15eb3665c196db13125fb4d88 100644
--- a/test/test_functional/test_prepare.py
+++ b/test/test_functional/test_prepare.py
@@ -117,9 +117,10 @@ def test_main_not_only_mash_infoexists():
max_dist = 0.06
verbose = 2
quiet = False
- prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_refseq,
- db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist, max_dist,
- verbose, quiet)
+ out_info_file = os.path.join(outdir, "LSTINFO-104099-filtered-0.0001_0.06.txt")
+ assert prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir,
+ threads, no_refseq, db_dir, only_mash, info_file, l90, nbcont,
+ cutn, min_dist, max_dist, verbose, quiet) == out_info_file
# Check output files
summary = os.path.join(GENEPATH, "assembly_summary-104099.txt")
@@ -316,9 +317,10 @@ def test_main_norefseq_nodefault_dbdir_but_refseq(capsys):
verbose = 2
quiet = False
info_file = ""
- prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_refseq,
- db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist, max_dist,
- verbose, quiet)
+ out_info_file = os.path.join(outdir, f"LSTINFO-123-filtered-0.0001_0.06.txt")
+ assert prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads,
+ no_refseq, db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist,
+ max_dist, verbose, quiet) == out_info_file
out, err = capsys.readouterr()
assert ("You asked to skip refseq downloads") in err
assert ("Database folder test/data/prepare/generated_by_func-tests/"
@@ -372,9 +374,10 @@ def test_main_norefseq_defaultdbdir(capsys):
verbose = 2
quiet = False
info_file = ""
- prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_refseq,
- db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist, max_dist,
- verbose, quiet)
+ out_info_file = os.path.join(outdir, "LSTINFO-123-filtered-0.0001_0.06.txt")
+ assert prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads,
+ no_refseq, db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist,
+ max_dist, verbose, quiet) == out_info_file
out, err = capsys.readouterr()
assert ("You asked to skip refseq downloads") in err
assert ("Total number of genomes for 123: 5") in out
@@ -421,9 +424,10 @@ def test_main_norefseq_givendbdir(capsys):
verbose = 2
quiet = False
info_file = ""
- prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_refseq,
- db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist, max_dist,
- verbose, quiet)
+ out_info_file = os.path.join(outdir, "LSTINFO-NA-filtered-0.0001_0.06.txt")
+ assert prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads,
+ no_refseq, db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist,
+ max_dist, verbose, quiet) == out_info_file
out, err = capsys.readouterr()
assert ("You asked to skip refseq downloads") in err
assert ("Total number of genomes for NA: 5") in out
@@ -462,9 +466,10 @@ def test_only_mash(capsys):
max_dist = 0.06
verbose = 1
quiet = False
- prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads, no_refseq,
- db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist, max_dist,
- verbose, quiet)
+ out_info_file = os.path.join(outdir, "LSTINFO-NA-filtered-0.0001_0.06.txt")
+ assert prepare.main("cmd", NCBI_species, NCBI_taxid, levels, outdir, tmp_dir, threads,
+ no_refseq, db_dir, only_mash, info_file, l90, nbcont, cutn, min_dist,
+ max_dist, verbose, quiet) == out_info_file
out, err = capsys.readouterr()
assert ("You asked to run only mash steps") in err
assert ("You want to run only mash steps. Getting information from "
diff --git a/test/test_unit/test_prepare/test_filter.py b/test/test_unit/test_prepare/test_filter.py
index b47a4932edfead06ff763c448b174ba2db1639b0..86d907fb252f355b1b9f3f172e2f220b87e194ed 100755
--- a/test/test_unit/test_prepare/test_filter.py
+++ b/test/test_unit/test_prepare/test_filter.py
@@ -124,11 +124,12 @@ def test_write_output():
max_dist = 0.06
# Check everything works without error
+ list_file = os.path.join(outdir, "LSTINFO-Acetobacter_fabarum-filtered-0.0001_0.06.txt")
assert filterg.write_outputfiles(genomes, sorted_genomes,
- genomes_removed, outdir, gspecies, min_dist, max_dist) == 0
+ genomes_removed, outdir, gspecies,
+ min_dist, max_dist) == list_file
# Check outfiles exist
- list_file = os.path.join(outdir, "LSTINFO-Acetobacter_fabarum-filtered-0.0001_0.06.txt")
discard_file = os.path.join(outdir, "discarded-by-minhash-Acetobacter_fabarum-0.0001_0.06.txt")
assert os.path.isfile(list_file)
assert os.path.isfile(discard_file)
@@ -181,11 +182,12 @@ def test_write_output_no_discard():
max_dist = 0.06
# Check everything works without error
+ list_file = os.path.join(outdir, "LSTINFO-Acetobacter_fabarum-filtered-0.0001_0.06.txt")
assert filterg.write_outputfiles(genomes, sorted_genomes,
- genomes_removed, outdir, gspecies, min_dist, max_dist) == 0
+ genomes_removed, outdir, gspecies,
+ min_dist, max_dist) == list_file
# Check outfiles exist
- list_file = os.path.join(outdir, "LSTINFO-Acetobacter_fabarum-filtered-0.0001_0.06.txt")
discard_file = os.path.join(outdir, "discarded-by-minhash-Acetobacter_fabarum-0.0001_0.06.txt")
assert os.path.isfile(list_file)
assert os.path.isfile(discard_file)
@@ -231,11 +233,12 @@ def test_write_output_no_genome():
max_dist = 0.06
# Check everything works without error
+ list_file = os.path.join(outdir, "LSTINFO-Acetobacter_fabarum-filtered-0.0001_0.06.txt")
assert filterg.write_outputfiles(genomes, sorted_genomes,
- genomes_removed, outdir, gspecies, min_dist, max_dist) == 0
+ genomes_removed, outdir, gspecies,
+ min_dist, max_dist) == list_file
# Check outfiles exist
- list_file = os.path.join(outdir, "LSTINFO-Acetobacter_fabarum-filtered-0.0001_0.06.txt")
discard_file = os.path.join(outdir, "discarded-by-minhash-Acetobacter_fabarum-0.0001_0.06.txt")
assert os.path.isfile(list_file)
assert os.path.isfile(discard_file)