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!')
import psycopg2
from flask import Flask, request, jsonify
from flask_cors import CORS, cross_origin
from psycopg2 import sql
from ingest import ingest
from annotate import Annotate
from extract import WebDriver
app = Flask(__name__)
cors = CORS(app)
annotate = Annotate()
webdriver = WebDriver()
webdriver.visit("http://localhost:3000")
def setup():
with psycopg2.connect("host=localhost") as conn:
with conn.cursor() as cur:
cur.execute("""
create table if not exists metamapper (
uri text,
field text,
xpath text,
value text,
primary key (uri, field)
);
""")
args = parser.parse_args()
classes_file=args.classes_file
annotation_dir=args.annotation_dir
output_dir = args.output_dir
image_file = args.image_file
mapper = get_mapper(classes_file)
files=[]
if image_file:
files.append(image_file)
else:
for f in os.listdir(annotation_dir):
if annotation_dir[:-1] =='/':
files.append(annotation_dir+f)
else:
files.append(annotation_dir + '/' + f)
if output_dir:
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
a = Annotate(files, mapper, save_folder=output_dir)
#annotation_file is always turned into a list
for f in a.annotation_file:
obj_key = a.get_objects(f)
# image labels generated
a.label_image(obj_key)
