dataset 1st2nd codons partitioned by each codon

VoSeq · Aug 24, 2015 · 6591671 · 6591671
1 parent a838212
commit 6591671
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Showing 3 changed files with 28 additions and 1 deletion.
diff --git a/voseq/create_dataset/dataset.py b/voseq/create_dataset/dataset.py
@@ -436,7 +436,16 @@ def from_seq_objs_to_dataset(self):
         if '1st' in self.codon_positions and '2nd' in self.codon_positions and \
                 '3rd' not in self.codon_positions and \
                 'ALL' not in self.codon_positions and \
-                'EACH' in self.partition_by_positions:
+                'EACH' in self.partition_by_positions and \
+                self.file_format == 'PHY':
+            self.partition_list = self.get_codons_in_one_partition(['1st', '2nd'])
+            return self.convert_lists_to_dataset(self.partition_list)
+
+        if '1st' in self.codon_positions and '2nd' in self.codon_positions and \
+                '3rd' not in self.codon_positions and \
+                'ALL' not in self.codon_positions and \
+                'EACH' in self.partition_by_positions and \
+                self.file_format != 'PHY':
             self.partition_list = self.get_codons_in_each_partition(['1st', '2nd'])
             return self.convert_lists_to_dataset(self.partition_list)
 

diff --git a/voseq/create_dataset/phylip.py b/voseq/create_dataset/phylip.py
@@ -102,6 +102,11 @@ def make_charset_line(self, count_start, count_end, gene):
             if len(self.codon_positions) == 1 and '3rd' in self.codon_positions:
                 line = 'DNA, {}_pos3 = {}-{}'.format(gene, count_start + 1, count_end)
                 return line
+            if len(self.codon_positions) == 2 and \
+                    '1st' in self.codon_positions and \
+                    '2nd' in self.codon_positions:
+                line = 'DNA, {}_pos12 = {}-{}'.format(gene, count_start + 1, count_end)
+                return line
 
     def convert_lists_to_dataset(self, partitions):
         """

diff --git a/voseq/create_dataset/tests/create_phylip_dataset/tests_create_phylip_dataset.py b/voseq/create_dataset/tests/create_phylip_dataset/tests_create_phylip_dataset.py
@@ -380,6 +380,19 @@ def test_dataset_1st2nd_codon_partitioned_one(self):
             expected = handle.read()
         self.assertEqual(expected, result)
 
+    def test_dataset_1st2nd_codon_partitioned_each(self):
+        cleaned_data = self.cleaned_data.copy()
+        cleaned_data['partition_by_positions'] = 'EACH'
+        cleaned_data['positions'] = ['1st', '2nd']
+        dataset_creator = CreateDataset(cleaned_data)
+        result = dataset_creator.dataset_str
+
+        dataset_file = os.path.join(settings.BASE_DIR, '..', 'create_dataset',
+                                    'tests', 'create_phylip_dataset', 'dataset_1st2nd_codons.phy')
+        with open(dataset_file, "r") as handle:
+            expected = handle.read()
+        self.assertEqual(expected, result)
+
     def test_charset_block_dataset_1st2nd_codon_partitioned_one(self):
         cleaned_data = self.cleaned_data.copy()
         cleaned_data['partition_by_positions'] = 'ONE'