metaquast: cosmetic-feature: --no-krona option added (workaround for #…

…216, #237, #246, #251)

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>

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:

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',

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")