def get_summary_object_for_profile_db(self,
profile_db_path,
init_gene_coverages=True):
collection_name = self.descriptions.genomes[
self.unique_profile_db_path_to_internal_genome_name[
profile_db_path][0]]['collection_id']
profile_db_path = self.descriptions.genomes[
self.unique_profile_db_path_to_internal_genome_name[
profile_db_path][0]]['profile_db_path']
contigs_db_path = self.descriptions.genomes[
self.unique_profile_db_path_to_internal_genome_name[
profile_db_path][0]]['contigs_db_path']
# poor-man's whatever
bin_names_list = [
self.descriptions.genomes[g]['bin_id'] for g in self.
unique_profile_db_path_to_internal_genome_name[profile_db_path]
]
ARGS = summarizer.ArgsTemplateForSummarizerClass()
ARGS.profile_db = profile_db_path
ARGS.contigs_db = contigs_db_path
ARGS.skip_init_functions = True
ARGS.init_gene_coverages = init_gene_coverages
ARGS.collection_name = collection_name
ARGS.bin_names_list = bin_names_list
ARGS.output_dir = None
summary = summarizer.ProfileSummarizer(ARGS)
summary.init()
summary.init_collection_profile(collection_name)
return summary
def gen_summary(args, d, request, response, collection_name):
set_default_headers(response)
if args.read_only:
return json.dumps({'error': "Sorry! This is a read-only instance."})
if d.manual_mode:
return json.dumps({
'error':
"Creating summaries is only possible with proper anvi'o runs at the moment :/"
})
run.info_single('A summary of collection "%s" has been requested.' %
collection_name)
# get a dummy args instance, and fill it down below
summarizer_args = summarizer.ArgsTemplateForSummarizerClass()
# common params. we will set pan/profile specific params a bit later:
summarizer_args.collection_name = collection_name
summarizer_args.taxonomic_level = d.taxonomic_level
if d.mode == 'pan':
summarizer_args.pan_db = d.pan_db_path
summarizer_args.genomes_storage = d.genomes_storage_path
summarizer_args.output_dir = os.path.join(
os.path.dirname(summarizer_args.pan_db),
'SUMMARY_%s' % collection_name)
elif d.mode == 'full':
summarizer_args.profile_db = d.profile_db_path
summarizer_args.contigs_db = d.contigs_db_path
summarizer_args.output_dir = os.path.join(
os.path.dirname(summarizer_args.profile_db),
'SUMMARY_%s' % collection_name)
else:
return json.dumps({
'error':
'We do not know anything about this mode: "%s"' % d.mode
})
# call the summary:
try:
summary = summarizer.PanSummarizer(
summarizer_args, r=run,
p=progress) if d.mode == 'pan' else summarizer.ProfileSummarizer(
summarizer_args, r=run, p=progress)
summary.process()
except Exception as e:
return json.dumps({
'error':
'Something failed in the "%s" summary mode. This is what we know: %s'
% (d.mode, e)
})
run.info_single('HTML output for summary is ready: %s' %
summary.index_html)
path = "summary/%s/index.html" % (collection_name)
return json.dumps({'path': path})
def init_pan_summary(self):
self.progress.new('Pan summary')
self.progress.update('Initializing...')
args = summarizer.ArgsTemplateForSummarizerClass()
args.pan_db = self.pan_db_path
args.genomes_storage = self.genomes_storage_path
args.skip_check_collection_name = True
args.skip_init_functions = True
self.pan_summary = summarizer.PanSummarizer(args)
self.progress.end()