From 1400ab41cdc586fafa838dd896532b0a17754b5a Mon Sep 17 00:00:00 2001
From: Kirill Bessonov <kbessonov@gmail.com>
Date: Fri, 22 Dec 2023 23:19:17 -0500
Subject: [PATCH] updated unit tests

---
 mob_suite/tests/test_mobrecon.py                     | 11 ++++++-----
 mob_suite/tests/test_mobtyper.py                     |  6 ++++--
 mob_suite/tests/test_mobtyper_vs_biomarker_report.py |  7 +++++--
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/mob_suite/tests/test_mobrecon.py b/mob_suite/tests/test_mobrecon.py
index 3a16cd4..9d9d446 100644
--- a/mob_suite/tests/test_mobrecon.py
+++ b/mob_suite/tests/test_mobrecon.py
@@ -7,13 +7,13 @@
 LOG_FORMAT = '%(asctime)s %(levelname)s: %(message)s [in %(pathname)s:%(lineno)d]'
 logging.basicConfig(format=LOG_FORMAT, level=logging.DEBUG)
 
-if not os.path.exists(os.path.join(TEST_ROOT,"run_test")):
-    os.mkdir(os.path.join(TEST_ROOT,"run_test"))
+def check_if_output_dir_exists_and_create():
+    if not os.path.exists(os.path.join(TEST_ROOT,"run_test")):
+        os.mkdir(os.path.join(TEST_ROOT,"run_test"))
 
 
 def test_mob_recon_with_mob_typer_report():
-    if os.path.exists("run_test") == False:
-        os.mkdir("run_test")
+    check_if_output_dir_exists_and_create()
     #IncFIB,IncFII multi-plasmids
     args = [
         "--infile", os.path.dirname(__file__) + "/TestData/Pseudomonas/test_contigs.fasta",
@@ -28,7 +28,7 @@ def test_mob_recon_with_mob_typer_report():
     assert sum(1 for line in open(mobtyper_results_file)) == 2 , "Results file is empty, something went wrong"
 
 def test_mob_recon_no_plasmid_biomarkers():
-
+    check_if_output_dir_exists_and_create()
     args = [
         "--infile", ROOT_MODULE + "/example/assembly_no_biomarkers.fasta",
         "--outdir", TEST_ROOT + "/run_test/mob_recon_no_plasmid_markers",
@@ -41,6 +41,7 @@ def test_mob_recon_no_plasmid_biomarkers():
     assert os.path.exists(os.path.join(TEST_ROOT,"run_test/mob_recon_no_plasmid_markers/biomarker_report.txt")) == False
 
 def test_mob_recon_typical_run():
+    check_if_output_dir_exists_and_create()
     args = [
         "--infile", ROOT_MODULE + "/example/SRR3703080_illumina_unicycler.fasta",
         "--outdir", TEST_ROOT+"/run_test/mob_recon_SRR3703080",
diff --git a/mob_suite/tests/test_mobtyper.py b/mob_suite/tests/test_mobtyper.py
index 20d0aa1..973f518 100644
--- a/mob_suite/tests/test_mobtyper.py
+++ b/mob_suite/tests/test_mobtyper.py
@@ -9,11 +9,13 @@
 logger=logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
 
+def check_if_output_dir_exists_and_create():
+    if not os.path.exists(os.path.join(TEST_ROOT,"run_test")):
+        os.mkdir(os.path.join(TEST_ROOT,"run_test"))
 
 def test_mean_and_multireplicon_frame():
     logger.info("Testing MOB-typer")
-    if os.path.exists("run_test") == False:
-        os.mkdir("run_test")
+    check_if_output_dir_exists_and_create()
     args = [
         "--infile", os.path.dirname(__file__) + "/TestData/pCAV1453-208.fasta",
         "--out_file", TEST_ROOT + "/run_test/mobtyper_pCAV1453-208_results.txt",
diff --git a/mob_suite/tests/test_mobtyper_vs_biomarker_report.py b/mob_suite/tests/test_mobtyper_vs_biomarker_report.py
index 096d8eb..ab613b0 100644
--- a/mob_suite/tests/test_mobtyper_vs_biomarker_report.py
+++ b/mob_suite/tests/test_mobtyper_vs_biomarker_report.py
@@ -23,10 +23,13 @@
 def clean_missing_dashes(L):
     return [i for i in L if i != '-']
 
+def check_if_output_dir_exists_and_create():
+    if not os.path.exists(os.path.join(TEST_ROOT,"run_test")):
+        os.mkdir(os.path.join(TEST_ROOT,"run_test"))
+
 
 def test_mean_and_multireplicon_frame(mode = None):
-    if os.path.exists("run_test") == False:
-        os.mkdir("run_test")
+    check_if_output_dir_exists_and_create()
 
     if mode == None:
         return 0