tiny-count: support for sequence-based read counting

START_HERE/paths.yml

@@ -7,7 +7,7 @@
 #   1. Fill out the Samples Sheet with files to process + naming scheme. [samples.csv]
 #   2. Fill out the Features Sheet with selection rules [features.csv]
 #   3. Set samples_csv and features_csv (below) to point to these files
-#   4. Add annotation files and per-file alias preferences to gff_files
+#   4. Add annotation files and per-file alias preferences to gff_files (optional)
 #
 ######-------------------------------------------------------------------------------######
 

tests/testdata/config_files/paths.yml

@@ -7,7 +7,7 @@
 #   1. Fill out the Samples Sheet with files to process + naming scheme. [samples.csv]
 #   2. Fill out the Features Sheet with selection rules [features.csv]
 #   3. Set samples_csv and features_csv (below) to point to these files
-#   4. Add annotation files and per-file alias preferences to gff_files
+#   4. Add annotation files and per-file alias preferences to gff_files (optional)
 #
 ######-------------------------------------------------------------------------------######
 

tests/unit_tests_configuration.py

@@ -286,18 +286,29 @@ def test_validate_required_parameters(self):
 
             config[key] = oldval
 
-    """Does PathsFile check that at least one GFF file has been provided?"""
+    """Does PathsFile notify the user of the change in counting style 
+    when no GFF files have been provided?"""
 
-    def test_validate_gff_files(self):
+    def test_no_gff_files(self):
         config = make_paths_file()
+        stdout = io.StringIO()
 
-        with self.assertRaisesRegex(AssertionError, r".*(At least one GFF).*"):
-            config['gff_files'] = [{'path': "", 'alias': []}]
-            config.validate_paths()
+        gff_configs = [
+            [{'path': "", 'alias': []}],
+            [{'irrelevant': "value"}],
+            None,
+            []
+        ]
 
-        with self.assertRaisesRegex(AssertionError, r".*(At least one GFF).*"):
-            config['gff_files'] = [{'irrelevant': "value"}]
-            config.validate_paths()
+        with contextlib.redirect_stdout(stdout):
+            for gff_config in gff_configs:
+                config['gff_files'] = gff_config
+                config.validate_paths()
+                config_return = config.get_gff_config()
+
+                self.assertRegex(stdout.getvalue(), r".*(No GFF files).*")
+                self.assertEqual(config_return, {})
+                stdout.truncate(0)
 
     """Does PathsFile check for missing files for single entry parameters?"""
 
@@ -350,6 +361,37 @@ def test_pipeline_mapping(self):
         self.assertEqual(config['empty_path'], "")
         self.assertEqual(config['none_path'], None)
 
+    """Does get_gff_config properly screen for "ID" alias attributes?"""
+
+    def test_get_gff_config_id_alias_attr(self):
+        config = make_paths_file()
+        config['gff_files'] = [{'path': "/irrelevant", 'alias': ['ID']}]
+
+        gff_files = config.get_gff_config()
+        expected = {"/irrelevant": []}
+
+        self.assertDictEqual(gff_files, expected)
+
+    """Does get_gff_config merge aliases if the same GFF file is listed more than once? 
+    Are duplicates also removed and original order preserved?"""
+
+    def test_get_gff_config_merge_alias_attr(self):
+        config = make_paths_file()
+        config['gff_files'] = [
+            {'path': "/same/path", 'alias': ['attr1', 'attr2']},
+            {'path': "/same/path", 'alias': ['attr1', 'attrN']},
+            {'path': "/different/path", 'alias': ['attr3']}
+        ]
+
+        gff_files = config.get_gff_config()
+
+        expected = {
+            "/same/path": ['attr1', 'attr2', 'attrN'],
+            "/different/path": ['attr3']
+        }
+
+        self.assertDictEqual(gff_files, expected)
+
 
 class ConfigurationTest(unittest.TestCase):
 

tests/unit_tests_counter.py

@@ -231,40 +231,6 @@ def test_load_config_rna_to_cDNA(self):
 
         self.assertEqual(ruleset[0]['nt5end'], 'T')
 
-    """Does load_gff_files properly screen for "ID" alias attributes?"""
-
-    def test_load_gff_files_id_alias_attr(self):
-        config = helpers.make_paths_file()
-        config['gff_files'] = [{'path': "/irrelevant", 'alias': ['ID']}]
-
-        # Patch GFFValidator so that it isn't called (not relevant)
-        with patch('tiny.rna.counter.counter.GFFValidator'):
-            gff_files = counter.load_gff_files(config, [], {})
-
-        expected = {"/irrelevant": []}
-        self.assertDictEqual(gff_files, expected)
-
-    """Does load_gff_files merge aliases if the same GFF file is listed more than once? 
-    Are duplicates also removed and original order preserved?"""
-
-    def test_load_gff_files_merge_alias_attr(self):
-        config = helpers.make_paths_file()
-        config['gff_files'] = [
-            {'path': "/same/path", 'alias': ['attr1', 'attr2']},
-            {'path': "/same/path", 'alias': ['attr1', 'attrN']},
-            {'path': "/different/path", 'alias': ['attr3']}
-        ]
-
-        # Patch GFFValidator so that it isn't called (not relevant)
-        with patch('tiny.rna.counter.counter.GFFValidator'):
-            gff_files = counter.load_gff_files(config, [], {})
-
-        expected = {
-            "/same/path": ['attr1', 'attr2', 'attrN'],
-            "/different/path": ['attr3']
-        }
-
-        self.assertDictEqual(gff_files, expected)
 
 if __name__ == '__main__':
     unittest.main()