added unit test for keeplength option

rescript/plugin_setup.py

@@ -1071,7 +1071,7 @@
         'primer_rev': 'Reverse primer used to find the end position '
                       'for alignment trimming. Provide as 5\'-3\'.',
         'position_start': 'Position within the alignment where the trimming '
-                          'will begin. If not provided, alignment will not'
+                          'will begin. If not provided, alignment will not '
                           'be trimmed at the beginning. If forward primer is'
                           'specified this parameter will be ignored.',
         'position_end': 'Position within the alignment where the trimming '

rescript/tests/data/small-silva-v4-trim-no-keeplength.fasta

@@ -0,0 +1,10 @@
+>AB299544.1.1336 Bacteria;Firmicutes;Clostridia;Oscillospirales;Ruminococcaceae;uncultured;uncultured Clostridiales bacterium
+----------------------------------------------------T-A--G----G--G--A---AT-AA-C--AT-------------------------T-T-G-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>JF826529.1.1310 Bacteria;Proteobacteria;Gammaproteobacteria;Burkholderiales;Alcaligenaceae;Achromobacter;Achromobacter sp. NS014
+----------------------------------------------------C-G--G----G--G--G---AT-AA-C--TA-------------------------C-C-C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>CP011401.2356993.2358524 Bacteria;Proteobacteria;Gammaproteobacteria;Burkholderiales;Alcaligenaceae;Bordetella;Bordetella pertussis
+----------------------------------------------------C-G--G----G--G--G---AT-AA-C--TA-------------------------C-G-C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>HM446088.1.1410 Bacteria;Cyanobacteria;Cyanobacteriia;Synechococcales;Cyanobiaceae;Cyanobium PCC-6307;uncultured bacterium
+----------------------------------------------------A-G--G----G--G--G---AT-AA-C--GG-------------------------C-T-G-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
+>FJ484772.1.1316 Bacteria;Proteobacteria;Gammaproteobacteria;Acidiferrobacterales;Acidiferrobacteraceae;Sulfurifustis;uncultured proteobacterium
+----------------------------------------------------T-G--G----G--G--G---AC-AA-C--CC-------------------------G-G-C-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

rescript/tests/test_trim_alignment.py

@@ -8,6 +8,7 @@
 
 
 import qiime2
+import skbio
 from qiime2.plugin.testing import TestPluginBase
 from q2_types.feature_data import (
     AlignedDNAFASTAFormat,
@@ -33,6 +34,12 @@ def aln2(self, *args, **kwargs):
     def aln3(self, *args, **kwargs):
         return [self.alignments[3]]
 
+    def aln4(self, *args, **kwargs):
+        return [self.alignments[4]]
+
+    def aln5(self, *args, **kwargs):
+        return [self.alignments[5]]
+
     def get_action(self, which_alignment):
         return getattr(self, f"aln{which_alignment}")
 
@@ -43,22 +50,59 @@ class TestExtractAlignmentRegion(TestPluginBase):
     def setUp(self):
         super().setUp()
 
-        aligned_seqs_fp = self.get_data_path('trim-test-alignment.fasta')
-        aligned_with_primers_fp = self.get_data_path(
-            'trim-test-alignment-with-primers.fasta')
+        aligned_silva_seqs_fp = self.get_data_path(
+            'small-silva-full-len-alignment.fasta')
+        self.aligned_silva_seqs = AlignedDNAFASTAFormat(
+             aligned_silva_seqs_fp, mode='r')
+
+        self.v4_primers_dict = {
+            "forward": "GTGYCAGCMGCCGCGGTAA",
+            "reverse": "GGACTACNVGGGTWTCTAAT"
+        }
 
+        silva_alignment_fp = self.get_data_path(
+            'small-silva-full-len-alignment.fasta')
+        self.silva_alignment = AlignedDNAFASTAFormat(
+            silva_alignment_fp, mode='r')
+
+        silva_alignment_v4_trim_keeplen_w_primers_fp = self.get_data_path(
+            'small-silva-v4-trim-keeplength-with-primers.fasta')
+        self.silva_v4_trim_keeplen_w_primers = AlignedDNAFASTAFormat(
+            silva_alignment_v4_trim_keeplen_w_primers_fp, mode='r')
+
+        silva_alignment_v4_trim_no_keeplen_w_primers_fp = self.get_data_path(
+            'small-silva-v4-trim-no-keeplength-with-primers.fasta')
+        self.silva_v4_trim_no_keeplen_w_primers = AlignedDNAFASTAFormat(
+            silva_alignment_v4_trim_no_keeplen_w_primers_fp, mode='r')
+
+        silva_alignment_v4_trim_keeplen_wo_primers_fp = self.get_data_path(
+            'small-silva-v4-trim-keeplength.fasta')
+        self.silva_v4_trim_keeplen = AlignedDNAFASTAFormat(
+            silva_alignment_v4_trim_keeplen_wo_primers_fp, mode='r')
+
+        silva_alignment_v4_trim_no_keeplen_wo_primers_fp = self.get_data_path(
+            'small-silva-v4-trim-no-keeplength.fasta')
+        self.silva_v4_trim_no_keeplen = AlignedDNAFASTAFormat(
+            silva_alignment_v4_trim_no_keeplen_wo_primers_fp, mode='r')
+
+        aligned_seqs_fp = self.get_data_path('trim-test-alignment.fasta')
         self.aligned_seqs = qiime2.Artifact.import_data(
             'FeatureData[AlignedSequence]', aligned_seqs_fp)
         self.aligned_seqs_fasta = AlignedDNAFASTAFormat(
             aligned_seqs_fp, mode='r')
+
         self.primers_dict = {
             "forward": "GGGAATCTTCCACAATGG",
             "reverse": "GTGTTCTTCTCTAACAACAG"
         }
+
+        aligned_with_primers_fp = self.get_data_path(
+            'trim-test-alignment-with-primers.fasta')
         self.aligned_with_primers = qiime2.Artifact.import_data(
             'FeatureData[AlignedSequence]', aligned_with_primers_fp)
         self.aligned_with_primers_fasta = AlignedDNAFASTAFormat(
             aligned_with_primers_fp, mode='r')
+
         self.aligned_mess_fasta = AlignedDNAFASTAFormat(
             self.get_data_path(
                 'trim-test-alignment-with-primers-mess.fasta'), mode='r')
@@ -71,7 +115,9 @@ def setUp(self):
 
         self.fake_ctx = FakeCtx({1: self.aligned_with_primers_fasta,
                                  2: self.aligned_with_fwd_fasta,
-                                 3: self.aligned_with_rev_fasta})
+                                 3: self.aligned_with_rev_fasta,
+                                 4: self.silva_v4_trim_no_keeplen_w_primers,
+                                 5: self.silva_v4_trim_keeplen_w_primers})
 
         self.exp_seqs_both_primers = {
             's1': ('GGGAATCTTCCACAATGGGTGCAAACCTGATGGAGCAATGCCGCGTGAG'
@@ -237,16 +283,39 @@ def test_trim_all_sequences_no_rev(self):
                     for seq in obs.view(DNAIterator)}
         self.assertDictEqual(obs_seqs, self.exp_seqs_only_fwd)
 
-    # test trimming when both primers are given
-    def test_trim_alignment(self):
-        obs = _trim_alignment(
-            self.fake_ctx.get_action(1),
-            self.aligned_seqs_fasta,
-            self.primers_dict["forward"],
-            self.primers_dict["reverse"])
-        obs_seqs = {seq.metadata['id']: str(seq)
-                    for seq in obs.view(DNAIterator)}
-        self.assertDictEqual(obs_seqs, self.exp_seqs_both_primers)
+    # test trimming when both primers are given and keeplength = False
+    # tests against expected alignment length
+    def test_trim_alignment_keeplen_false(self):
+        obs_v4_nokeep_aln = _trim_alignment(
+            self.fake_ctx.get_action(4),
+            self.aligned_silva_seqs,
+            self.v4_primers_dict["forward"],
+            self.v4_primers_dict["reverse"],
+            keeplength=False)
+
+        obs_aln = skbio.io.read(str(obs_v4_nokeep_aln), into=skbio.TabularMSA,
+                                constructor=skbio.DNA)
+        exp_aln = skbio.io.read(str(self.silva_v4_trim_no_keeplen),
+                                into=skbio.TabularMSA,
+                                constructor=skbio.DNA)
+        self.assertEqual(obs_aln, exp_aln)
+
+    # test trimming when both primers are given and keeplength = True
+    # tests against expected alignment length
+    def test_trim_alignment_keeplen_true(self):
+        obs_v4_keep_aln = _trim_alignment(
+            self.fake_ctx.get_action(5),
+            self.aligned_silva_seqs,
+            self.v4_primers_dict["forward"],
+            self.v4_primers_dict["reverse"],
+            keeplength=True)
+
+        obs_aln = skbio.io.read(str(obs_v4_keep_aln), into=skbio.TabularMSA,
+                                constructor=skbio.DNA)
+        exp_aln = skbio.io.read(str(self.silva_v4_trim_keeplen),
+                                into=skbio.TabularMSA,
+                                constructor=skbio.DNA)
+        self.assertEqual(obs_aln, exp_aln)
 
     # test trimming when only fwd primer is given
     def test_trim_alignment_only_fwd(self):

rescript/trim_alignment.py

@@ -191,7 +191,8 @@ def _trim_alignment(expand_alignment_action,
                     primer_rev=None,
                     position_start=None,
                     position_end=None,
-                    n_threads=1) -> AlignedDNAFASTAFormat:
+                    n_threads=1,
+                    keeplength=True) -> AlignedDNAFASTAFormat:
     """
     Trim alignment based on primer alignment or explicitly specified
     positions. When at least one primer sequence is given, primer-based
@@ -231,8 +232,8 @@ def _trim_alignment(expand_alignment_action,
             alignment=aligned_sequences,
             sequences=primers,
             addfragments=True,
-            keeplength=True,
-            n_threads=n_threads)
+            n_threads=n_threads,
+            keeplength=keeplength)
 
         # find trim positions based on primer positions within alignment
         trim_positions = _locate_primer_positions(alignment_with_primers)