Merge with c2pro

edilytics · Mar 21, 2024 · 31430c7 · 31430c7
1 parent 2de605f
commit 31430c7
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Showing 3 changed files with 17 additions and 7 deletions.
diff --git a/CRISPResso2/CRISPRessoBatchCORE.py b/CRISPResso2/CRISPRessoBatchCORE.py
@@ -16,8 +16,10 @@
 from CRISPResso2 import CRISPRessoShared
 try:
     from CRISPRessoPro import plot as CRISPRessoPlot
+    pro_installed = True
 except:
     from CRISPResso2 import CRISPRessoPlot
+    pro_installed = False
 from CRISPResso2 import CRISPRessoMultiProcessing
 from CRISPResso2.CRISPRessoReports import CRISPRessoReport
 
@@ -119,6 +121,12 @@ def main():
 
         _jp = lambda filename: os.path.join(OUTPUT_DIRECTORY, filename) #handy function to put a file in the output directory
 
+        if args.use_matplotlib or not pro_installed:
+            from CRISPResso2 import CRISPRessoPlot
+        else:
+            from CRISPRessoPro import plot as CRISPRessoPlot
+        CRISPRessoPlot.setMatplotlibDefaults()
+
         try:
             info('Creating Folder %s' % OUTPUT_DIRECTORY, {'percent_complete': 0})
             os.makedirs(OUTPUT_DIRECTORY)

diff --git a/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py b/CRISPResso2/CRISPRessoReports/CRISPRessoReport.py
@@ -268,11 +268,12 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
 
     summary_plot_htmls = {}
     for plot_name in window_nuc_pct_quilts + nuc_pct_quilts:
-        with open(os.path.join(batch_folder, f'{plot_name}.json')) as window_nuc_pct_json_fh:
-            summary_plot_htmls[plot_name] = f"""
-        <div class="d-flex justify-content-between" style="max-height: 80vh; overflow-y: auto;" id="{plot_name}"></div>
-        <script type="text/javascript">const {plot_name} = {window_nuc_pct_json_fh.read().strip()}</script>
-        """
+        if os.path.exists(os.path.join(batch_folder, f'{plot_name}.json')):
+            with open(os.path.join(batch_folder, f'{plot_name}.json')) as window_nuc_pct_json_fh:
+                summary_plot_htmls[plot_name] = f"""
+            <div class="d-flex justify-content-between" style="max-height: 80vh; overflow-y: auto;" id="{plot_name}"></div>
+            <script type="text/javascript">const {plot_name} = {window_nuc_pct_json_fh.read().strip()}</script>
+            """
 
     #find path between the report and the data (if the report is in another directory vs in the same directory as the data)
     crispresso_data_path = os.path.relpath(batch_folder, os.path.dirname(crispressoBatch_report_file))
@@ -325,6 +326,7 @@ def make_batch_report_from_folder(crispressoBatch_report_file, crispresso2_info,
         nuc_conv_plots=nuc_conv_plots,
         allele_modification_heatmap_plot=allele_modification_heatmap_plot,
         allele_modification_line_plot=allele_modification_line_plot,
+        pro_installed=pro_installed,
     )
 
 
@@ -507,7 +509,7 @@ def fill_default(dictionary, key, default_type=list):
             dictionary[key] = default_type()
 
     j2_env = Environment(
-        loader=FileSystemLoader(os.path.join(_ROOT, 'CRISPRessoReports', 'templates')),
+        loader=FileSystemLoader([os.path.join(_ROOT, 'CRISPRessoReports', 'templates'), os.path.join(_ROOT, "CRISPRessoPro", "templates")]),
     )
     j2_env.filters['dirname'] = dirname
     if crispresso_tool == 'batch':

diff --git a/CRISPResso2/CRISPRessoReports/templates/batchReport.html b/CRISPResso2/CRISPRessoReports/templates/batchReport.html
@@ -267,6 +267,6 @@ <h5>{{allele_modification_heatmap_plot_titles[heatmap_plot_name]}}</h5>
 {% block foot %}
 {% if pro_installed %}
   <script src="https://unpkg.com/d3@5"></script>
-  {{ render_partial('shared/partials/batch_d3.html', nucleotide_quilt_slugs=(window_nuc_pct_quilts + nuc_pct_quilts))}}
+  {{ render_partial('partials/batch_d3.html', nucleotide_quilt_slugs=(window_nuc_pct_quilts + nuc_pct_quilts))}}
 {% endif %}
 {% endblock %}