From 3bbd2e404bf39ffcf755be788e41651648cd0046 Mon Sep 17 00:00:00 2001
From: Amandine PERRIN <amandine.perrin@pasteur.fr>
Date: Thu, 10 Dec 2020 16:00:42 +0100
Subject: [PATCH] adapt test to new param names
---
test/test_functional/test_annote.py | 2 +-
test/test_functional/test_prepare.py | 6 +++---
.../test_annotate/test_annotation_functions-prokka.py | 2 +-
3 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/test/test_functional/test_annote.py b/test/test_functional/test_annote.py
index f56e520e..81486699 100755
--- a/test/test_functional/test_annote.py
+++ b/test/test_functional/test_annote.py
@@ -621,7 +621,7 @@ def test_main_prodigal_ok(capsys):
os.makedirs(res_folder)
# Function arguments
- list_file = os.path.join(TEST_DIR, "list_genomes.txt")
+ list_file = os.path.join(GENEPATH, "list_genomes.txt")
with open(list_file, "w") as lf:
lf.write("A_H738.fasta \n")
lf.write("H299_H561.fasta::TOTO")
diff --git a/test/test_functional/test_prepare.py b/test/test_functional/test_prepare.py
index d04ee928..8128dc4e 100644
--- a/test/test_functional/test_prepare.py
+++ b/test/test_functional/test_prepare.py
@@ -55,15 +55,15 @@ def test_main_from_parse():
"""
args = argparse.Namespace()
args.argv = ["prepare", "test_func_prepare"]
- args.NCBI_species = "Acetobacter orleanensis"
- args.NCBI_species_taxid = "104099"
+ args.ncbi_species = "Acetobacter orleanensis"
+ args.ncbi_species_taxid = "104099"
args.outdir = GENEPATH
args.tmp_dir = ""
args.parallel = 1
args.no_refseq = False
args.db_dir = ""
args.only_mash = False
- args.from_info = ""
+ args.info_file = ""
args.l90 = 100
args.nbcont = 999
args.cutn = 0
diff --git a/test/test_unit/test_annotate/test_annotation_functions-prokka.py b/test/test_unit/test_annotate/test_annotation_functions-prokka.py
index 19eb2ea5..aab5d729 100644
--- a/test/test_unit/test_annotate/test_annotation_functions-prokka.py
+++ b/test/test_unit/test_annotate/test_annotation_functions-prokka.py
@@ -77,7 +77,7 @@ def test_check_prokka_no_outdir():
Test that prokka returns the right error message when output directory does not exist
"""
logger = my_logger("test_check_prokka_no_outdir")
- outdir = "outdir"
+ outdir = os.path.join(GENEPATH, "outdir")
name = "prokka_out_for_test"
logf = "prokka.log"
gpath = os.path.join(GENEPATH, "toto.fna")
--
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