Merge 7e8cc9f into 28c2081

qiime2 · Jun 8, 2018 · aa5c418 · aa5c418
2 parents 28c2081 + 7e8cc9f
commit aa5c418
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diff --git a/q2_demux/_summarize/_visualizer.py b/q2_demux/_summarize/_visualizer.py
@@ -95,6 +95,17 @@ def _compute_stats_of_df(df):
     return df_stats
 
 
+def _build_seq_len_table(qscores: pd.Series) -> str:
+    sequence_lengths = qscores.notnull().sum(axis=1).copy()
+    sequence_length_stats = _compute_stats_of_df(sequence_lengths)
+
+    sequence_length_stats.rename(index={'50%': '50% (Median)',
+                                        'count': 'Total Sequences Sampled'},
+                                 inplace=True)
+    frame = sequence_length_stats.to_frame(name="")
+    return q2templates.df_to_html(frame)
+
+
 def summarize(output_dir: str, data: _PlotQualView, n: int=10000) -> None:
     paired = data.paired
     data = data.directory_format
@@ -152,19 +163,24 @@ def summarize(output_dir: str, data: _PlotQualView, n: int=10000) -> None:
     forward_stats.to_csv(os.path.join(output_dir,
                          'forward-seven-number-summaries.csv'),
                          header=True, index=True)
+    forward_length_table = _build_seq_len_table(forward_scores)
 
     if (forward_stats.loc['50%'] > 45).any():
         dangers.append('Some of the PHRED quality values are out of range. '
                        'This is likely because an incorrect PHRED offset '
                        'was chosen on import of your raw data. You can learn '
                        'how to choose your PHRED offset during import in the '
                        'importing tutorial.')
+
+    # Required initilization for conditional display of the table
+    reverse_length_table = None
     if paired:
         reverse_scores = pd.DataFrame(quality_scores['reverse'])
         reverse_stats = _compute_stats_of_df(reverse_scores)
         reverse_stats.to_csv(os.path.join(output_dir,
                              'reverse-seven-number-summaries.csv'),
                              header=True, index=True)
+        reverse_length_table = _build_seq_len_table(reverse_scores)
 
     show_plot = len(fwd) > 1
     if show_plot:
@@ -187,7 +203,10 @@ def summarize(output_dir: str, data: _PlotQualView, n: int=10000) -> None:
             'max': result.max(),
             'sum': sequence_count
         },
+        'forward_length_table': forward_length_table,
+        'reverse_length_table': reverse_length_table,
         'result': html,
+        'n_samples': result.count(),
         'show_plot': show_plot,
         'paired': paired,
         'tabs': [{'title': 'Overview',

diff --git a/q2_demux/_summarize/assets/overview.html b/q2_demux/_summarize/assets/overview.html
@@ -25,9 +25,28 @@ <h1>Demultiplexed sequence counts summary</h1>
 </div>
 {% endif %}
 
+<div class="row">
+    <div class="col-lg-12">
+        <h1>Demultiplexed sequence length summary</h1>
+        {% set colsize = 6 if reverse_length_table else 12 %}
+        <div class="col-lg-{{ colsize }}">
+            <h4>Forward Reads</h4>
+            {{ forward_length_table }}
+        </div>
+        {% if reverse_length_table %}
+        <div class="col-lg-{{ colsize }}">
+            <h4>Reverse Reads</h4>
+            {{ reverse_length_table }}
+        </div>
+        {% endif %}
+    </div>
+</div>
+
+
 <div class="row">
     <div class="col-lg-12">
         <h1>Per-sample sequence counts</h1>
+        <h4>Total Samples: {{ n_samples }}</h4>
         {{ result }}
         <a href="per-sample-fastq-counts.csv">Download as CSV</a>
     </div>