BUG: handle single end of reverse reads in summarize (#118)

Co-authored-by: Evan Bolyen <ebolyen@gmail.com>

q2_demux/_summarize/_visualizer.py

@@ -115,7 +115,9 @@ def summarize(output_dir: str, data: _PlotQualView, n: int = 10000) -> None:
 
     manifest = data.manifest.view(pd.DataFrame)
 
-    directions = ['forward', 'reverse'] if paired else ['forward']
+    columns = list(manifest.columns)
+
+    directions = columns
     file_records = {'forward': [], 'reverse': []}
     per_sample_fastq_counts = {'forward': {}, 'reverse': {}}
     subsample_size = {'forward': n, 'reverse': n}
@@ -132,7 +134,7 @@ def summarize(output_dir: str, data: _PlotQualView, n: int = 10000) -> None:
             # If we have an empty direction for a sample that will be a nan in
             # the manifest. Skip that nan
             if type(filename) != str:
-                if np.isnan(filename):
+                if filename is None or np.isnan(filename):
                     continue
 
             for seq in _read_fastq_seqs(filename):

q2_demux/_summarize/assets/overview.html

@@ -1,11 +1,7 @@
 {% extends "tab-child.html" %}
 
 {% block content %}
-{% if paired %}
-    {% set directions = ['forward', 'reverse'] %}
-{% else %}
-    {% set directions = ['forward'] %} 
-{% endif %}
+{% set directions = ['forward', 'reverse'] %}
 
 <div class="row">
     <div class="col-lg-12">
@@ -29,7 +25,7 @@ <h3>{{ direction|capitalize }} Reads Frequency Histogram</h3>
                 {% endif %}
             </div>
         </div>
-    {% endfor %} 
+    {% endfor %}
 </div>
 
 <div class="row">

q2_demux/tests/data/reverse_only/MANIFEST

@@ -0,0 +1,2 @@
+sample-id,filename,direction
+sample2,sample2_2_L001_R2_001.fastq.gz,reverse

q2_demux/tests/data/reverse_only/metadata.yml

@@ -0,0 +1,2 @@
+phred-offset: 33
+

q2_demux/tests/test_demux.py

@@ -1180,6 +1180,14 @@ def test_warnings_per_direction(self):
                 self.assertIn('greater than the amount of sequences across all'
                               ' samples for the reverse reads', html)
 
+    def test_only_reverse_reads(self):
+        reverse = SingleLanePerSampleSingleEndFastqDirFmt(
+            self.get_data_path('reverse_only'), mode='r')
+        with tempfile.TemporaryDirectory() as output_dir:
+            summarize(output_dir, _PlotQualView(reverse, paired=False), n=1)
+        # Checkpoint assertion
+        self.assertTrue(True)
+
     def test_empty_single_end(self):
         empty = SingleLanePerSampleSingleEndFastqDirFmt(
             self.get_data_path('summarize_empty/empty_single_end'), mode='r')

setup.py

@@ -42,6 +42,7 @@
                            'data/summarize_empty/empty_forward_in_paired/*',
                            'data/summarize_empty/empty_reverse_in_paired/*',
                            'data/summarize_empty/empty_paired_end/*'
+                           'data/reverse_only/*'
                            ],
         'q2_demux': ['_summarize/assets/*.html',
                      '_summarize/assets/dist/*',