def make_cat_root(args):
cat_root = QCCategory(
'root',
html_head='<h1>QC Report</h1><hr>',
map_key_desc=MAP_KEY_DESC_GENERAL
)
# add general information dict to cat_root
d_general = OrderedDict([
('date', now()),
('title', args.title),
('description', args.desc),
('pipeline_ver', args.pipeline_ver),
('pipeline_type', args.pipeline_type),
('genome', args.genome),
('paired_end', args.paired_ends),
('aligner', args.aligner),
('peak_caller', args.peak_caller),
])
if args.ctl_paired_ends \
and args.pipeline_type not in ('atac', 'dnase'):
d_general['ctl_paired_end'] = args.ctl_paired_ends
cat_root.add_log(d_general, key='general')
return cat_root
def make_cat_root(args):
cat_root = QCCategory('root',
html_head='<h1>QC Report</h1><hr>',
map_key_desc=MAP_KEY_DESC_GENERAL)
# add general information dict to cat_root
d_general = dict([
('date', now()),
('title', args.title),
('description', args.desc),
('pipeline_ver', args.pipeline_ver),
('pipeline_type', args.pipeline_type),
('genome', args.genome),
('aligner', args.aligner),
('seq_endedness', {}),
('peak_caller', args.peak_caller),
])
if args.paired_ends is not None:
for i, paired_end in enumerate(args.paired_ends):
d_general['seq_endedness']['rep{}'.format(i + 1)] = {
'paired_end': paired_end
}
if args.ctl_paired_ends is not None:
for i, paired_end in enumerate(args.ctl_paired_ends):
d_general['seq_endedness']['ctl{}'.format(i + 1)] = {
'paired_end': paired_end
}
cat_root.add_log(d_general, key='general')
return cat_root