From fef570d1b19510185c1f16bceaca64a93749b194 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Fri, 16 Oct 2020 19:18:19 +0200
Subject: [PATCH] add first test for prepare/only_mash
---
.../exp_files/exp_lstinfo_run_only-mash.lst | 2 +
.../test_files/test_lstinfo_onlymash.lst | 6 +++
test/test_functional/test_prepare.py | 45 +++++++++++++++++++
3 files changed, 53 insertions(+)
create mode 100644 test/data/prepare/exp_files/exp_lstinfo_run_only-mash.lst
create mode 100644 test/data/prepare/test_files/test_lstinfo_onlymash.lst
diff --git a/test/data/prepare/exp_files/exp_lstinfo_run_only-mash.lst b/test/data/prepare/exp_files/exp_lstinfo_run_only-mash.lst
new file mode 100644
index 00000000..9015579e
--- /dev/null
+++ b/test/data/prepare/exp_files/exp_lstinfo_run_only-mash.lst
@@ -0,0 +1,2 @@
+to_annotate gsize nb_conts L90
+test/data/prepare/genomes/genomes_comparison/ACOC.1019.fna 3050 1 1
diff --git a/test/data/prepare/test_files/test_lstinfo_onlymash.lst b/test/data/prepare/test_files/test_lstinfo_onlymash.lst
new file mode 100644
index 00000000..3265e383
--- /dev/null
+++ b/test/data/prepare/test_files/test_lstinfo_onlymash.lst
@@ -0,0 +1,6 @@
+to_annotate gsize nb_conts L90
+test/data/prepare/genomes/genomes_comparison/ACOC.1019.fna 3050 1 1
+test/data/prepare/genomes/genomes_comparison/ACOR002.0519.fna 3012665 78 17
+test/data/prepare/genomes/genomes_comparison/ACOR001.0519-almost-same.fna 3012665 261 17
+test/data/prepare/genomes/genomes_comparison/ACOR001.0519.fna 3012665 269 17
+test/data/prepare/genomes/genomes_comparison/ACOR001.0519-bis.fna 3012665 269 17
diff --git a/test/test_functional/test_prepare.py b/test/test_functional/test_prepare.py
index 44930301..f60f3d72 100644
--- a/test/test_functional/test_prepare.py
+++ b/test/test_functional/test_prepare.py
@@ -440,3 +440,48 @@ def test_main_norefseq_givendbdir(capsys):
tmp_files = glob.glob(os.path.join(GENEPATH, "tmp_files", "*.fna_prepare-split2N.fna"))
assert len(tmp_files) == 5
+
+def test_only_mash(capsys):
+ """
+ Running only mash step (giving genomes and corresponding LSTINFO file)
+ """
+ NCBI_species = ""
+ NCBI_taxid = ""
+ levels = ""
+ outdir = GENEPATH
+ tmp_dir = ""
+ threads = 1
+ no_refseq = False
+ db_dir = ""
+ only_mash = True
+ info_file = os.path.join(TEST_DIR, "test_lstinfo_onlymash.lst")
+ l90 = 100
+ nbcont = 999
+ cutn = 5
+ min_dist = 1e-4
+ 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, err = capsys.readouterr()
+ assert ("You asked to run only mash steps") in err
+ assert ("You want to run only mash steps. Getting information from "
+ "test/data/prepare/test_files/test_lstinfo_onlymash.lst") in out
+ assert ("Found 5 genomes in total") in out
+ assert ("Computing pairwise distances between all genomes") in out
+ assert ("Sorting all 5 genomes by quality") in out
+ assert ("Final number of genomes in dataset: 1") in out
+
+ # Check output files
+ assert len(os.listdir(os.path.join(outdir, "tmp_files"))) == 0
+ # Check logfiles are here
+ log_files = glob.glob(os.path.join(outdir, "*log*"))
+ assert len(log_files) == 3
+ # Check content of output lstinfo file
+ out_lst = os.path.join(outdir, "LSTINFO-NA-filtered-0.0001_0.06.txt")
+ exp_lst = os.path.join(DBDIR, "exp_files", "exp_lstinfo_run_only-mash.lst")
+ assert tutil.compare_order_content(out_lst, exp_lst)
+
+
--
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