WiP - Expanding uses of attributes for scoring

This is a tentative approach at expanding the uses of attributes as part of the scoring, includes a minimal test case but is still missing other categories for these could be present (not_fragmentary and the main requirements), currently these are only tested for the scoring section and minimally with this commit for the as_requirements section.

Mikado/loci/locus.py

@@ -580,9 +580,13 @@ def _check_as_requirements(self, transcript: Transcript, is_reference=False) ->
         evaluated = dict()
         for key in section.parameters:
             name = section.parameters[key].name
-            value = operator.attrgetter(name)(transcript)
-            if "external" in key:
-                value = value[0]
+            if 'attributes' in name:
+                name_parts = name.split('.')
+                value = transcript.attributes[name_parts[1]]
+            else:
+                value = operator.attrgetter(name)(transcript)
+                if "external" in key:
+                    value = value[0]
 
             evaluated[key] = self.evaluate(value, section.parameters[key])
             # pylint: disable=eval-used

Mikado/tests/test_external_scores.py

@@ -2,7 +2,7 @@
 import unittest
 
 from .. import create_default_logger
-from .._transcripts.scoring_configuration import ScoringFile, MinMaxScore
+from .._transcripts.scoring_configuration import ScoringFile, MinMaxScore, SizeFilter
 from ..loci import Transcript, Superlocus
 import pkg_resources
 import os
@@ -185,3 +185,16 @@ def test_attribute_use_raw_percentage(self):
         sup.get_metrics()
         self.assertIn("attributes.tpm", sup._metrics[self.transcript.id])
         self.assertEqual(sup._metrics[self.transcript.id]["attributes.tpm"], 0.1)
+        sup.define_loci()
+
+    def test_attribute_use_as_alternative_splicing(self):
+        from Mikado.loci import Locus
+        checked_conf = self.conf.copy()
+        self.transcript.attributes['cov'] = 10
+        loci = Locus(self.transcript, configuration=checked_conf)
+        loci.configuration.scoring.as_requirements.parameters['attributes.cov'] = SizeFilter(operator='ge', value=3,
+                                                                                             metric=None,
+                                                                                             name='attributes.cov')
+        loci.configuration.scoring.as_requirements.expression = [
+            loci.configuration.scoring.as_requirements.expression[0] + ' and attributes.cov']
+        loci._check_as_requirements(self.transcript)