Other tests for EI-CoreBioinformatics#137

Mikado/loci/sublocus.py

@@ -84,13 +84,15 @@ def __init__(self,
 
         if isinstance(transcript_instance, Transcript):
             self.add_transcript_to_locus(transcript_instance)
+            self.attributes = transcript_instance.attributes.copy()
+            self.parent = transcript_instance.parent
         else:
-            self.parent = getattr(transcript_instance, "parent")
+            self.parent = getattr(transcript_instance, "parent", None)
             self.chrom = getattr(transcript_instance, "chrom")
             self.start = getattr(transcript_instance, "start")
             self.end = getattr(transcript_instance, "end")
             self.strand = getattr(transcript_instance, "strand")
-            self.attributes = getattr(transcript_instance, "attributes")
+            self.attributes = getattr(transcript_instance, "attributes", dict())
 
         self.monosubloci = []
         self.logger.debug("Initialized {0}".format(self.id))

Mikado/picking/picker.py

@@ -861,7 +861,7 @@ def __submit_multi_threading(self, data_dict):
                 elif row.is_transcript is True:
                     if current_transcript is not None and invalid is False:
                         self.__test_sortedness(row, current_transcript)
-                        if Superlocus.in_locus(
+                        if current_locus is not None and Superlocus.in_locus(
                                 current_locus, current_transcript,
                                 flank=self.json_conf["pick"]["clustering"]["flank"]) is True:
                             current_locus.add_transcript_to_locus(current_transcript,
@@ -893,7 +893,7 @@ def __submit_multi_threading(self, data_dict):
                         intron_range=intron_range)
 
         if current_transcript is not None and invalid is False:
-            if Superlocus.in_locus(
+            if current_locus is not None and Superlocus.in_locus(
                     current_locus, current_transcript,
                     flank=self.json_conf["pick"]["clustering"]["flank"]) is True:
                 current_locus.add_transcript_to_locus(
@@ -1030,7 +1030,7 @@ def __submit_single_threaded(self, data_dict):
                 elif row.is_transcript is True:
                     if current_transcript is not None and invalid is False:
                         self.__test_sortedness(row, current_transcript)
-                        if Superlocus.in_locus(
+                        if current_locus is not None and Superlocus.in_locus(
                                 current_locus, current_transcript,
                                 flank=self.json_conf["pick"]["clustering"]["flank"]) is True:
                             current_locus.add_transcript_to_locus(current_transcript,
@@ -1071,7 +1071,7 @@ def __submit_single_threaded(self, data_dict):
                         intron_range=intron_range, logger=logger)
 
         if current_transcript is not None and invalid is False:
-            if Superlocus.in_locus(
+            if current_locus is not None and Superlocus.in_locus(
                     current_locus, current_transcript,
                     flank=self.json_conf["pick"]["clustering"]["flank"]) is True:
                 current_locus.add_transcript_to_locus(

Mikado/tests/locus_test.py

@@ -161,6 +161,24 @@ def test_evaluate_overlap(self):
             self.assertFalse(child1._evaluate_transcript_overlap(self.transcript1, self.transcript2)[0])
             self.assertTrue(child1._evaluate_transcript_overlap(self.transcript1, self.transcript1)[0])
 
+    def test_invalid_sublocus(self):
+
+        with self.assertRaises(ValueError):
+            self.transcript1.json_conf = None
+            _ = Sublocus(self.transcript1, json_conf=None)
+
+        with self.assertRaises(FileNotFoundError):
+            _ = Sublocus(self.transcript1, json_conf="test")
+
+    def test_sublocus_from_sublocus(self):
+
+        s = Sublocus(self.transcript1)
+        s2 = Sublocus(s)
+        self.assertFalse(s.fixed_size)
+        self.assertTrue(s2.fixed_size)
+        for attr in ["parent", "chrom", "start", "end", "strand", "attributes"]:
+            self.assertEqual(getattr(s, attr), getattr(s2, attr))
+
 
 class LocusTester(unittest.TestCase):