From 5775f20e67b071c664e00317d7259f180cda1721 Mon Sep 17 00:00:00 2001 From: "A. Murat Eren" Date: Wed, 4 Apr 2012 16:29:11 -0400 Subject: [PATCH] new command line parameter: --gen-dataset-oligo-networks. it is better 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. --- oligotyping.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/oligotyping.py b/oligotyping.py index 04b401d..eecaadf 100755 --- a/oligotyping.py +++ b/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.')