def enrichment(self, en_path):
"""Nothing here yet"""
print("Populating Enrichments..")
if en_path:
en_list = glob.glob(en_path + '*.yml')
else:
en_dir = ATCconfig.get('enrichments_directory')
en_list = glob.glob(en_dir + '/*.yml')
for en_file in en_list:
try:
en = Enrichment(en_file,
apipath=self.apipath,
auth=self.auth,
space=self.space)
en.render_template("confluence")
confluence_data = {
"title":
en.en_parsed_file['title'],
"spacekey":
self.space,
"parentid":
str(
ATCutils.confluence_get_page_id(
self.apipath, self.auth, self.space,
"Enrichments")),
"confluencecontent":
en.content,
}
res = ATCutils.push_to_confluence(confluence_data,
self.apipath, self.auth)
if res == 'Page updated':
print("==> updated page: EN '" +
en.en_parsed_file['title'] + "'")
# print("Done: ", en.en_parsed_file['title'])
except Exception as err:
print(en_file + " failed")
print("Err message: %s" % err)
print('-' * 60)
traceback.print_exc(file=sys.stdout)
print('-' * 60)
print("Enrichments populated!")
def enrichment(self, en_path):
"""Nothing here yet"""
if en_path:
en_list = glob.glob(en_path + '*.yml')
else:
en_list = glob.glob('../enrichments/*.yml')
for en_file in en_list:
try:
en = Enrichment(en_file)
en.render_template("markdown")
en.save_markdown_file(atc_dir=self.atc_dir)
except Exception as e:
print(en_file + " failed\n\n%s\n\n" % e)
print("Err message: %s" % e)
print('-' * 60)
traceback.print_exc(file=sys.stdout)
print('-' * 60)
def enrichment(self, en_path):
"""Populate Enrichments"""
print("Populating Enrichments..")
if en_path:
en_list = glob.glob(en_path + '*.yml')
else:
en_dir = ATCconfig.get('enrichments_directory')
en_list = glob.glob(en_dir + '/*.yml')
for en_file in en_list:
try:
en = Enrichment(en_file)
en.render_template("markdown")
en.save_markdown_file(atc_dir=self.atc_dir)
except Exception as e:
print(en_file + " failed\n\n%s\n\n" % e)
print("Err message: %s" % e)
print('-' * 60)
traceback.print_exc(file=sys.stdout)
print('-' * 60)
print("Enrichments populated!")
def main(self, args, command):
'''
Parameters
----------
Output
------
'''
self._check_general(args)
self._logging_setup(args)
logging.info("Running command: %s" % ' '.join(command))
if args.subparser_name == self.DATA:
self._check_data(args)
d = Data()
d.do()
if args.subparser_name == self.ANNOTATE:
self._check_annotate(args)
a = Annotate(# Define inputs and outputs
args.output,
# Define type of annotation to be carried out
args.ko,
args.pfam,
args.tigrfam,
args.cog,
args.hypothetical,
# Cutoffs
args.evalue,
args.bit,
args.id,
args.aln_query,
args.aln_reference,
args.cascaded,
args.c,
# Parameters
args.threads,
args.parallel,
args.suffix)
a.do(args.genome_directory, args.protein_directory,
args.genome_files, args.protein_files)
elif args.subparser_name == self.CLASSIFY:
self._check_classify(args)
c = Classify()
c.do(args.custom_modules,
args.cutoff,
args.genome_and_annotation_file,
args.genome_and_annotation_matrix,
args.output)
elif args.subparser_name == self.ENRICHMENT:
self._check_enrichment(args)
e = Enrichment()
e.do(# Inputs
args.annotation_matrix,
args.annotation_file,
args.metadata,
args.modules,
args.abundances,
args.do_all,
args.do_ivi,
args.do_gvg,
args.do_ivg,
args.pval_cutoff,
args.proportions_cutoff,
args.threshold,
args.multi_test_correction,
args.output)
elif args.subparser_name == self.COMPARE:
self._check_compare(args)
c = Compare()
c.do(args.enrichm_annotate_output)
elif(args.subparser_name == NetworkAnalyser.PATHWAY or
args.subparser_name == NetworkAnalyser.EXPLORE or
args.subparser_name == NetworkAnalyser.TRAVERSE):
self._check_network(args)
na=NetworkAnalyser(args.metadata)
na.do(args.matrix,
args.transcriptome,
args.metabolome,
args.depth,
args.filter,
args.limit,
args.queries,
args.subparser_name,
args.starting_compounds,
args.steps,
args.number_of_queries,
args.output)
logging.info('Done!')