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new command line parameter: --gen-dataset-oligo-networks. it is bette…

…r to keep this optional since these figures take too much time to generate, take too much space to store, and they have relatively little insight to offer.
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commit 5775f20e67b071c664e00317d7259f180cda1721 1 parent fddb3fb
@meren authored
Showing with 4 additions and 1 deletion.
  1. +4 −1 oligotyping.py
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5 oligotyping.py
@@ -71,6 +71,7 @@ def __init__(self, args = None):
self.no_display = args.no_display
self.skip_blast_search = args.skip_blast_search
self.gen_html = args.gen_html
+ self.gen_dataset_oligo_networks = args.gen_dataset_oligo_networks
self.datasets_dict = {}
self.datasets = []
@@ -205,7 +206,7 @@ def run_all(self):
if not self.quick:
self._generate_representative_sequences()
self._generate_random_colors()
- if (not self.no_figures) and (not self.quick):
+ if ((not self.no_figures) and (not self.quick)) and self.gen_dataset_oligo_networks:
self._generate_dataset_oligotype_network_figures()
if not self.no_figures:
self._generate_stack_bar_figure()
@@ -595,6 +596,8 @@ def _generate_html_output(self):
help = 'When set, no figures will be shown.')
parser.add_argument('--gen-html', action = 'store_true', default = False,
help = 'Generate static HTML output to browse analysis results.')
+ parser.add_argument('--gen-dataset-oligo-networks', action = 'store_true', default = False,
+ help = 'Generate oligotype network structure figures for each dataset.')
parser.add_argument('--project', default = None, type=str,
help = 'When a project name is set, given name will be used in figures whenever possible.')
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