Improved a bit calls, as per EI-CoreBioinformatics#142 and EI-CoreBio…

…informatics#137

Mikado/configuration/configurator.py

@@ -661,6 +661,6 @@ def to_json(string, simple=False, logger=None):
         logger.exception(exc)
         with open("ERROR.{}".format("json" if string.endswith("json") else "yaml"), "wt") as errored:
             errored.write(open(string).read())
-        raise
+        raise OSError(exc)
 
     return json_dict

Mikado/tests/locus_test.py

@@ -185,6 +185,22 @@ class LocusTester(unittest.TestCase):
     logger = create_null_logger(inspect.getframeinfo(inspect.currentframe())[2])
     logger_name = logger.name
 
+    @classmethod
+    def setUpClass(cls):
+        cls.__genomefile__ = None
+
+        cls.__genomefile__ = tempfile.NamedTemporaryFile(mode="wb", delete=False, suffix=".fa", prefix="prepare")
+
+        with pkg_resources.resource_stream("Mikado.tests", "chr5.fas.gz") as _:
+            cls.__genomefile__.write(gzip.decompress(_.read()))
+        cls.__genomefile__.flush()
+        cls.fai = pyfaidx.Fasta(cls.__genomefile__.name)
+
+    @classmethod
+    def tearDownClass(cls):
+        os.remove(cls.__genomefile__.name)
+        os.remove(cls.fai.faidx.indexname)
+
     def setUp(self):
 
         gff_transcript1 = """Chr1\tfoo\ttranscript\t101\t400\t.\t+\t.\tID=t0
@@ -230,7 +246,9 @@ def setUp(self):
         # with self.assertRaises(exceptions.NoJsonConfigError):
         #     _ = Superlocus(self.transcript1)
         self.my_json = os.path.join(os.path.dirname(__file__), "configuration.yaml")
+
         self.my_json = configurator.to_json(self.my_json)
+        self.my_json["reference"]["genome"] = self.fai.filename
         self.assertIn("scoring", self.my_json, self.my_json.keys())
 
     def test_locus(self):
@@ -1102,6 +1120,22 @@ class TestLocus(unittest.TestCase):
 
     logger = Mikado.utilities.log_utils.create_default_logger("tester")
 
+    @classmethod
+    def setUpClass(cls):
+        cls.__genomefile__ = None
+
+        cls.__genomefile__ = tempfile.NamedTemporaryFile(mode="wb", delete=False, suffix=".fa", prefix="prepare")
+
+        with pkg_resources.resource_stream("Mikado.tests", "chr5.fas.gz") as _:
+            cls.__genomefile__.write(gzip.decompress(_.read()))
+        cls.__genomefile__.flush()
+        cls.fai = pyfaidx.Fasta(cls.__genomefile__.name)
+
+    @classmethod
+    def tearDownClass(cls):
+        os.remove(cls.__genomefile__.name)
+        os.remove(cls.fai.faidx.indexname)
+
     def setUp(self):
 
         """Set up for the unit test."""
@@ -1205,6 +1239,7 @@ def setUp(self):
         # self.logger = logging.getLogger("tester")
         # self.handler = logging.StreamHandler()
         self.logger.setLevel(logging.WARNING)
+        self.json_conf["reference"]["genome"] = self.fai.filename
         # self.logger.addHandler(self.handler)
 
     def test_validity(self):
@@ -1396,10 +1431,12 @@ def test_remove_AS_overlapping(self):
                                    "parameters": {
                                        "cdna_length": {"operator": "gt", "value": 0, "name": "cdna_length"}
                                    }}
+        conf["pick"]["alternative_splicing"]["pad"] = False
 
         with self.subTest():
             superlocus_one = Superlocus(t1, json_conf=conf)
             superlocus_one.add_transcript_to_locus(t1_1)
+
             locus_one = Locus(t1, json_conf=conf)
             locus_one.logger = logger
             superlocus_one.loci[locus_one.id] = locus_one

Mikado/tests/test_system_calls.py

@@ -613,7 +613,7 @@ def test_reference_selection(self):
             self.conf["prepare"]["files"]["labels"] = ["T1", "T2"]
 
             for round in rounds:
-                for iteration in range(4):  # Repeat each test 4 times
+                for iteration in range(2):  # Repeat each test 2 times, not more for time length reasons
                     with self.subTest(round=round, format=format, iteration=iteration,
                                       msg="Starting round {} ({})".format(round, rounds[round])):
                         t1_score, t2_score, is_ref, res, corr_strand = rounds[round]
@@ -703,7 +703,7 @@ def test_reference_cds_kept(self):
             self.conf["prepare"]["files"]["labels"] = ["T1", "T2"]
 
             for round in rounds:
-                for iteration in range(4):  # Repeat each test 4 times
+                for iteration in range(2):  # Repeat each test 2 times for time length reasons
                     with self.subTest(round=round, format=format, iteration=iteration,
                                       msg="Starting round {} ({})".format(round, rounds[round])):
                         t1_score, t2_score, is_ref, res, coding = rounds[round]
@@ -873,6 +873,7 @@ def test_stat(self):
                 namespace.gff.close()
                 dir.cleanup()
 
+
 class ConfigureCheck(unittest.TestCase):
 
     """Test for creating configuration files"""
@@ -1044,14 +1045,31 @@ class PickTest(unittest.TestCase):
     def setUp(self):
 
         self.json_conf = configurator.to_json(None)
+        self.json_conf["reference"]["genome"] = self.fai.filename
+
+    @classmethod
+    def setUpClass(cls):
+        cls.__genomefile__ = None
+
+        cls.__genomefile__ = tempfile.NamedTemporaryFile(mode="wb", delete=False, suffix=".fa", prefix="prepare")
+
+        with pkg_resources.resource_stream("Mikado.tests", "chr5.fas.gz") as _:
+            cls.__genomefile__.write(gzip.decompress(_.read()))
+        cls.__genomefile__.flush()
+        cls.fai = pyfaidx.Fasta(cls.__genomefile__.name)
+
+    @classmethod
+    def tearDownClass(cls):
+        os.remove(cls.__genomefile__.name)
+        os.remove(cls.fai.faidx.indexname)
 
     def test_single_proc(self):
 
         self.json_conf["pick"]["run_options"]["procs"] = 1
         self.json_conf["db_settings"]["db"] = pkg_resources.resource_filename("Mikado.tests", "mikado.db")
 
         self.json_conf["pick"]["files"]["input"] = pkg_resources.resource_filename("Mikado.tests",
-                                                                              "mikado_prepared.gtf")
+                                                                                   "mikado_prepared.gtf")
         dir = tempfile.TemporaryDirectory()
         self.json_conf["pick"]["files"]["output_dir"] = dir.name
         self.json_conf["pick"]["files"]["loci_out"] = "mikado.monoproc.loci.gff3"
@@ -1103,7 +1121,7 @@ def test_multi_proc(self):
     def test_subprocess(self):
 
         self.json_conf["pick"]["files"]["input"] = pkg_resources.resource_filename("Mikado.tests",
-                                                                              "mikado_prepared.gtf")
+                                                                                   "mikado_prepared.gtf")
         dir = tempfile.TemporaryDirectory()
         self.json_conf["pick"]["files"]["output_dir"] = dir.name
         self.json_conf["pick"]["files"]["loci_out"] = "mikado.subproc.loci.gff3"
@@ -1361,5 +1379,30 @@ def test_purging(self):
         dir.cleanup()
 
 
+class SerialiseChecker(unittest.TestCase):
+
+    def setUp(self):
+        self.json_conf = configurator.to_json(None)
+        self.json_conf["reference"]["genome"] = self.fai.filename
+
+    @classmethod
+    def setUpClass(cls):
+        cls.__genomefile__ = None
+
+        cls.__genomefile__ = tempfile.NamedTemporaryFile(mode="wb", delete=False, suffix=".fa", prefix="serialise")
+
+        with pkg_resources.resource_stream("Mikado.tests", "chr5.fas.gz") as _:
+            cls.__genomefile__.write(gzip.decompress(_.read()))
+        cls.__genomefile__.flush()
+        cls.fai = pyfaidx.Fasta(cls.__genomefile__.name)
+
+    @classmethod
+    def tearDownClass(cls):
+        os.remove(cls.__genomefile__.name)
+        os.remove(cls.fai.faidx.indexname)
+
+
+
+
 if __name__ == "__main__":
     unittest.main()

requirements.txt

@@ -2,17 +2,16 @@ wheel>=0.28.0
 pyyaml
 jsonschema
 cython>=0.25
-numpy>=1.15.0
+numpy>=1.16.0
 networkx>=2
 sqlalchemy>=1
 sqlalchemy_utils
 biopython>=1.70
 intervaltree
-nose  # for numpy tester
 pytest
 pyfaidx
 scikit-learn>=0.17.0
-scipy>=0.15.0
+scipy>=1.0.0
 frozendict
 python-magic
 drmaa

setup.cfg

@@ -2,5 +2,5 @@
 test=pytest
 
 [tool:pytest]
-addopts = --cov Mikado
+# addopts = --cov Mikado
 norecursedirs = datrie*