IMP: additional aligned sequence transformers (#248)

q2_types/feature_data/_transformer.py

@@ -262,6 +262,13 @@ def _dnafastaformats_to_metadata(ff):
     return qiime2.Metadata(df)
 
 
+def _series_to_fasta_format(ff, data):
+    with ff.open() as f:
+        for id_, seq in data.iteritems():
+            sequence = skbio.DNA(seq, metadata={'id': id_})
+            skbio.io.write(sequence, format='fasta', into=f)
+
+
 @plugin.register_transformer
 def _9(ff: DNAFASTAFormat) -> DNAIterator:
     generator = _read_dna_fasta(str(ff))
@@ -339,10 +346,7 @@ def _31(ff: DNAFASTAFormat) -> qiime2.Metadata:
 @plugin.register_transformer
 def _16(data: pd.Series) -> DNAFASTAFormat:
     ff = DNAFASTAFormat()
-    with ff.open() as f:
-        for id_, seq in data.iteritems():
-            sequence = skbio.DNA(seq, metadata={'id': id_})
-            skbio.io.write(sequence, format='fasta', into=f)
+    _series_to_fasta_format(ff, data)
     return ff
 
 
@@ -364,6 +368,24 @@ def _33(ff: AlignedDNAFASTAFormat) -> qiime2.Metadata:
     return _dnafastaformats_to_metadata(ff)
 
 
+@plugin.register_transformer
+def _34(ff: AlignedDNAFASTAFormat) -> pd.Series:
+    return _dnafastaformats_to_series(ff)
+
+
+@plugin.register_transformer
+def _35(data: pd.Series) -> AlignedDNAFASTAFormat:
+    ff = AlignedDNAFASTAFormat()
+    _series_to_fasta_format(ff, data)
+    return ff
+
+
+@plugin.register_transformer
+def _36(fmt: AlignedDNAFASTAFormat) -> DNAIterator:
+    generator = _read_dna_fasta(str(fmt))
+    return DNAIterator(generator)
+
+
 # differential types
 @plugin.register_transformer
 def _222(ff: DifferentialFormat) -> pd.DataFrame:

q2_types/feature_data/tests/test_transformer.py

@@ -694,6 +694,55 @@ def test_aligned_dnafasta_format_to_metadata(self):
 
         self.assertEqual(exp, obs)
 
+    def test_aligned_dnafasta_format_to_series(self):
+        _, obs = self.transform_format(AlignedDNAFASTAFormat, pd.Series,
+                                       'aligned-dna-sequences.fasta')
+
+        obs = obs.astype(str)
+
+        index = pd.Index(['SEQUENCE1', 'SEQUENCE2'])
+        exp = pd.Series(['------------------------ACGTACGTACGTACGTACGTAC'
+                         'GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',
+                         'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC'
+                         'GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT'],
+                        index=index, dtype=object)
+
+        assert_series_equal(exp, obs)
+
+    def test_series_to_aligned_dnafasta_format(self):
+        transformer = self.get_transformer(pd.Series, AlignedDNAFASTAFormat)
+
+        index = pd.Index(['SEQUENCE1', 'SEQUENCE2'])
+        input = pd.Series(['------------------------ACGTACGTACGTACGTACGTAC'
+                           'GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT',
+                           'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC'
+                           'GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT'],
+                          index=index, dtype=object)
+
+        obs = transformer(input)
+
+        self.assertIsInstance(obs, AlignedDNAFASTAFormat)
+
+        obs_lines = list(open(str(obs)))
+        self.assertEqual(obs_lines[0], '>SEQUENCE1\n')
+        self.assertEqual(obs_lines[1],
+                         '------------------------ACGTACGTACGTACGTACGTAC'
+                         'GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n')
+        self.assertEqual(obs_lines[2], '>SEQUENCE2\n')
+        self.assertEqual(obs_lines[3],
+                         'ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTAC'
+                         'GTACGTACGTACGTACGTACGTACGTACGTACGTACGTACGT\n')
+
+    def test_aligned_dna_fasta_format_to_dna_iterator(self):
+        input, obs = self.transform_format(
+            AlignedDNAFASTAFormat, DNAIterator,
+            filename='aligned-dna-sequences.fasta')
+
+        exp = skbio.read(str(input), format='fasta', constructor=skbio.DNA)
+
+        for observed, expected in zip(obs, exp):
+            self.assertEqual(observed, expected)
+
 
 class TestDifferentialTransformer(TestPluginBase):
     package = 'q2_types.feature_data.tests'