From 2723558fa28d8a72f8c0cadd4f5f75e1ad6e2e9c Mon Sep 17 00:00:00 2001
From: Alexey Gurevich <alexeigurevich@gmail.com>
Date: Fri, 8 Sep 2023 10:44:27 +0200
Subject: [PATCH] metaquast: cosmetic-feature: --no-krona option added
 (workaround for #216, #237, #246, #251)

---
 manual.html                         | 9 +++++++--
 quast_libs/html_saver/html_saver.py | 9 +++++----
 quast_libs/options_parser.py        | 6 +++++-
 quast_libs/qconfig.py               | 5 ++++-
 4 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/manual.html b/manual.html
index 358bd79d70..a729ea6690 100644
--- a/manual.html
+++ b/manual.html
@@ -781,7 +781,12 @@ <h3>2.3 Command line options</h3>
 <div class='option'>
 <code><a name='no_plots'></a><b>--no-plots</b></code>
 </div>
-Do not draw plots.
+Do not draw static plots (in the PDF format by default).
+
+<div class='option'>
+<code><a name='no_krona'></a><b>--no-krona</b></code>
+</div>
+Do not draw <a href="#krona_charts">Krona pie charts</a>. Note: these plots are created <b>only</b> in the MetaQUAST <i>de novo</i> evaluation mode (without reference genomes).
 
 <div class='option'>
 <code><b>--no-html</b></code>
@@ -1393,7 +1398,7 @@ <h3>3.3 MetaQUAST output</h3>
 </div>
 <p>Note that values for some metrics like # contigs may not sum up, because one contig may be aligned to multiple reference genomes.
     You may read an extended discussion and explanation of this effect in the case of # misassemblies in the <a href="https://github.com/ablab/quast/issues/158">corresponding GitHub issue</a>.</p>
-<p><span class='metric-name'>Krona charts</span><br>
+<p><a name='krona_charts'></a><span class='metric-name'>Krona charts</span><br>
     Krona pie charts show assemblies and dataset taxonomic profiles. Relative species abundance is calculated based on the <a href="#total_length">total aligned length</a> of contigs aligned to corresponding reference genome.
     Charts are created for each assembly and one additional chart is created for all assemblies altogether.<br>
     Note: these plots are created <b>only</b> in <i>de novo</i> evaluation mode (MetaQUAST without reference genomes).</p>
diff --git a/quast_libs/html_saver/html_saver.py b/quast_libs/html_saver/html_saver.py
index 1ef5eca459..b6f5901729 100644
--- a/quast_libs/html_saver/html_saver.py
+++ b/quast_libs/html_saver/html_saver.py
@@ -250,11 +250,12 @@ def create_meta_report(results_dirpath, json_texts):
     if not os.path.isfile(html_fpath):
         init(html_fpath, is_meta=True)
 
-    from quast_libs import search_references_meta
-    taxons_for_krona = search_references_meta.taxons_for_krona
     meta_log = get_logger(qconfig.LOGGER_META_NAME)
-    if taxons_for_krona:
-        create_krona_charts(taxons_for_krona, meta_log, results_dirpath, json_texts)
+    if qconfig.draw_krona:
+        from quast_libs import search_references_meta
+        taxons_for_krona = search_references_meta.taxons_for_krona
+        if taxons_for_krona:
+            create_krona_charts(taxons_for_krona, meta_log, results_dirpath, json_texts)
 
     # reading html template file
     with open(html_fpath) as f_html:
diff --git a/quast_libs/options_parser.py b/quast_libs/options_parser.py
index b40b3d021d..8c9dbe203b 100644
--- a/quast_libs/options_parser.py
+++ b/quast_libs/options_parser.py
@@ -654,7 +654,7 @@ def parse_options(logger, quast_args):
              action='callback',
              callback=set_multiple_variables,
              callback_kwargs={'store_true_values': ['no_gc', 'no_sv', 'no_read_stats'],
-                              'store_false_values': ['show_snps', 'draw_plots', 'html_report', 'create_icarus_html', 'analyze_gaps']},
+                              'store_false_values': ['show_snps', 'draw_plots', 'draw_krona', 'html_report', 'create_icarus_html', 'analyze_gaps']},
              default=False)
          ),
         # (['--no-gzip'], dict(
@@ -679,6 +679,10 @@ def parse_options(logger, quast_args):
              dest='draw_plots',
              action='store_false')
          ),
+        (['--no-krona'], dict(
+            dest='draw_krona',
+            action='store_false')
+         ),
         (['--no-html'], dict(
              dest='html_report',
              action='callback',
diff --git a/quast_libs/qconfig.py b/quast_libs/qconfig.py
index 1e7270cbd1..12551405ee 100644
--- a/quast_libs/qconfig.py
+++ b/quast_libs/qconfig.py
@@ -59,6 +59,7 @@
 split_scaffolds = False
 draw_plots = True
 draw_circos = False
+draw_krona = True
 html_report = True
 save_json = False
 metagenemark = False
@@ -516,7 +517,9 @@ def usage(show_hidden=False, mode=None, short=True, stream=sys.stdout):
         stream.write("\n")
         stream.write("Speedup options:\n")
         stream.write("    --no-check                        Do not check and correct input fasta files. Use at your own risk (see manual)\n")
-        stream.write("    --no-plots                        Do not draw plots\n")
+        stream.write("    --no-plots                        Do not draw static plots\n")
+        if mode == 'meta':
+            stream.write("    --no-krona                        Do not draw Krona pie charts (in the without references mode)\n")
         stream.write("    --no-html                         Do not build html reports and Icarus viewers\n")
         stream.write("    --no-icarus                       Do not build Icarus viewers\n")
         stream.write("    --no-snps                         Do not report SNPs (may significantly reduce memory consumption on large genomes)\n")