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)