rename param to addfragments

qiime2 · Nov 2, 2020 · 10b293d · 10b293d
1 parent 5c12aeb
commit 10b293d
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Showing 3 changed files with 11 additions and 9 deletions.
diff --git a/q2_alignment/_mafft.py b/q2_alignment/_mafft.py
@@ -26,7 +26,7 @@ def run_command(cmd, output_fp, verbose=True):
         subprocess.run(cmd, stdout=output_f, check=True)
 
 
-def _mafft(sequences_fp, alignment_fp, n_threads, parttree, fragments):
+def _mafft(sequences_fp, alignment_fp, n_threads, parttree, addfragments):
     # Save original sequence IDs since long ids (~250 chars) can be truncated
     # by mafft. We'll replace the IDs in the aligned sequences file output by
     # mafft with the originals.
@@ -92,7 +92,7 @@ def _mafft(sequences_fp, alignment_fp, n_threads, parttree, fragments):
         cmd += ['--parttree']
 
     if alignment_fp is not None:
-        add_flag = '--addfragments' if fragments else '--add'
+        add_flag = '--addfragments' if addfragments else '--add'
         cmd += [add_flag, sequences_fp, alignment_fp]
     else:
         cmd += [sequences_fp]
@@ -132,7 +132,8 @@ def mafft_add(alignment: AlignedDNAFASTAFormat,
               sequences: DNAFASTAFormat,
               n_threads: int = 1,
               parttree: bool = False,
-              fragments: bool = False) -> AlignedDNAFASTAFormat:
+              addfragments: bool = False) -> AlignedDNAFASTAFormat:
     alignment_fp = str(alignment)
     sequences_fp = str(sequences)
-    return _mafft(sequences_fp, alignment_fp, n_threads, parttree, fragments)
+    return _mafft(
+        sequences_fp, alignment_fp, n_threads, parttree, addfragments)
diff --git a/q2_alignment/plugin_setup.py b/q2_alignment/plugin_setup.py
@@ -47,7 +47,7 @@
             'sequences': FeatureData[Sequence]},
     parameters={'n_threads': Int % Range(1, None) | Str % Choices(['auto']),
                 'parttree': Bool,
-                'fragments': Bool},
+                'addfragments': Bool},
     outputs=[('expanded_alignment', FeatureData[AlignedSequence])],
     input_descriptions={'alignment': 'The alignment to which '
                                      'sequences should be added.',
@@ -57,8 +57,9 @@
                      'all available cores)',
         'parttree': 'This flag is required if the number of sequences being '
                     'aligned are larger than 1000000. Disabled by default',
-        'fragments': 'This flag indicates that alignment optimized for '
-                     'addition of fragmentary sequences should be used.'},
+        'addfragments': 'Optimize for the addition of short sequence '
+                        'fragments (for example, primer or amplicon '
+                        'sequences).'},
     output_descriptions={
         'expanded_alignment': 'Alignment containing the provided aligned and '
                               'unaligned sequences.'},

diff --git a/q2_alignment/tests/test_mafft.py b/q2_alignment/tests/test_mafft.py
@@ -117,7 +117,7 @@ def test_mafft_add_fragments(self):
         alignment, sequences, exp = self._prepare_sequence_data()
 
         with redirected_stdio(stderr=os.devnull):
-            result = mafft_add(alignment, sequences, fragments=True)
+            result = mafft_add(alignment, sequences, addfragments=True)
         obs = skbio.io.read(str(result), into=skbio.TabularMSA,
                             constructor=skbio.DNA)
         self.assertEqual(obs, exp)
@@ -133,7 +133,7 @@ def test_mafft_add_flags(self):
                     ["mafft", "--preservecase", "--inputorder", "--thread",
                      "1", "--add", ANY, ANY], ANY)
 
-                _ = mafft_add(alignment, sequences, fragments=True)
+                _ = mafft_add(alignment, sequences, addfragments=True)
                 patched_run_cmd.assert_called_with(
                     ["mafft", "--preservecase", "--inputorder", "--thread",
                      "1", "--addfragments", ANY, ANY], ANY)