From e492c10571399f3ddab2811e7c412e00550ae43e Mon Sep 17 00:00:00 2001
From: Luca Venturini <lucventurini@gmail.com>
Date: Wed, 10 Oct 2018 20:00:00 +0100
Subject: [PATCH] Implemented unit-test for #133

---
 Mikado/tests/test_system_calls.py             | 28 +++++++++++++++++++
 ...correctedness.fa => test_truncated_cds.fa} |  0
 ...rrectdness.gff => test_truncated_cds.gff3} |  0
 3 files changed, 28 insertions(+)
 rename Mikado/tests/{prepare_phase_correctedness.fa => test_truncated_cds.fa} (100%)
 rename Mikado/tests/{prepare_phase_correctdness.gff => test_truncated_cds.gff3} (100%)

diff --git a/Mikado/tests/test_system_calls.py b/Mikado/tests/test_system_calls.py
index cc1990c27..0ee08618f 100644
--- a/Mikado/tests/test_system_calls.py
+++ b/Mikado/tests/test_system_calls.py
@@ -419,6 +419,34 @@ def test_negative_cdna_redundant_cds_not(self):
 
                 self.assertGreater(coding_count, 0)
 
+    def test_truncated_cds(self):
+        files = ["test_truncated_cds.gff3"]
+        files = [pkg_resources.resource_filename("Mikado.tests", filename) for filename in files]
+        self.conf["prepare"]["files"]["gff"] = files
+        self.conf["prepare"]["files"]["labels"] = [""]
+        self.conf["prepare"]["files"]["output_dir"] = tempfile.gettempdir()
+        self.conf["prepare"]["files"]["out_fasta"] = "mikado_prepared.fasta"
+        self.conf["prepare"]["files"]["out"] = "mikado_prepared.gtf"
+        self.conf["prepare"]["strip_cds"] = False
+
+        self.conf["reference"]["genome"] = pkg_resources.resource_filename("Mikado.tests",
+                                                                           "test_truncated_cds.fa")
+        args = Namespace()
+        args.strip_cds = False
+        args.json_conf = self.conf
+        prepare.prepare(args, self.logger)
+        self.assertTrue(os.path.exists(os.path.join(self.conf["prepare"]["files"]["output_dir"],
+                                                    "mikado_prepared.fasta")))
+        fa = pyfaidx.Fasta(os.path.join(self.conf["prepare"]["files"]["output_dir"],
+                                        "mikado_prepared.fasta"))
+        self.assertEqual(len(fa.keys()), 1)
+        gtf_file = os.path.join(self.conf["prepare"]["files"]["output_dir"], "mikado_prepared.gtf")
+        lines = [line for line in to_gff(gtf_file)]
+        cds = [_ for _ in lines if _.feature == "CDS"]
+        self.assertEqual(len(cds), 1)
+        self.assertEqual(cds[0].frame, 1)
+        self.assertEqual(cds[0].phase, 2)
+
 
 class CompareCheck(unittest.TestCase):
 
diff --git a/Mikado/tests/prepare_phase_correctedness.fa b/Mikado/tests/test_truncated_cds.fa
similarity index 100%
rename from Mikado/tests/prepare_phase_correctedness.fa
rename to Mikado/tests/test_truncated_cds.fa
diff --git a/Mikado/tests/prepare_phase_correctdness.gff b/Mikado/tests/test_truncated_cds.gff3
similarity index 100%
rename from Mikado/tests/prepare_phase_correctdness.gff
rename to Mikado/tests/test_truncated_cds.gff3