def __main__(): print "Quality and somatic filtering script starts at: %s\n" % datetime.datetime.now() parser = argparse.ArgumentParser(description='Filter variants based on qulaity and somatic filters') parser.add_argument('-i','--input_file', help='specify input file', required=True) parser.add_argument('-f','--quality_somatic_filters', help='specify quality and somatic filters', required=True) parser.add_argument('-p','--pairing', help='specify if sample paired with matched normal: paired or unpaired', required=True) args = vars(parser.parse_args()) # variant_input_file = "bam_vcf_cnv_path.txt" variant_summary = args['input_file'] filters = args['quality_somatic_filters'] pairing = args['pairing'] filtered_summary = ".".join([variant_summary, "filtered.tmp" ]).replace('.txt', '') somatic_summary = ".".join([filtered_summary, "somatic.tmp"]).replace('.txt','') filter_variants(variant_summary, filters, pairing, filtered_summary, somatic_summary) # recalculate occurrence for filtered summary out = make_occurrence_dict(filtered_summary) gene_patients_occur = out[0] var_patients_occur = out[1] gene_variants_occur = out[2] calculate_occurrence(filtered_summary, gene_patients_occur, var_patients_occur, gene_variants_occur) # recalculate occurrence for somatic summary if (os.path.isfile(somatic_summary)): out = make_occurrence_dict(somatic_summary) gene_patients_occur = out[0] var_patients_occur = out[1] gene_variants_occur = out[2] calculate_occurrence(somatic_summary, gene_patients_occur, var_patients_occur, gene_variants_occur) os.reomve(somatic_summary) # remove intermediate files os.remove(filtered_summary)
def __main__(): logger.info("Quality and somatic filtering script starts at: %s\n" % datetime.datetime.now()) parser = argparse.ArgumentParser( description='Filter variants based on qulaity and somatic filters') parser.add_argument('-i', '--input_file', help='specify input file', required=True) parser.add_argument('-f', '--quality_somatic_filters', help='specify quality and somatic filters', required=True) parser.add_argument( '-p', '--pairing', help='specify if sample paired with matched normal: paired or unpaired', required=True) args = vars(parser.parse_args()) logger.debug('some debug message') logger.info('some info message') logger.warning('some warning message') logger.error('some error message') logger.critical('some critical message') # variant_input_file = "bam_vcf_cnv_path.txt" variant_summary = args['input_file'] filters = args['quality_somatic_filters'] pairing = args['pairing'] filtered_summary = ".".join([variant_summary, "filtered.tmp"]).replace('.txt', '') somatic_summary = ".".join([filtered_summary, "somatic.tmp"]).replace('.txt', '') filter_variants(variant_summary, filters, pairing, filtered_summary, somatic_summary) # recalculate occurrence for filtered summary out = make_occurrence_dict(filtered_summary) gene_patients_occur = out[0] var_patients_occur = out[1] gene_variants_occur = out[2] calculate_occurrence(filtered_summary, gene_patients_occur, var_patients_occur, gene_variants_occur) # recalculate occurrence for somatic summary if (os.path.isfile(somatic_summary)): out = make_occurrence_dict(somatic_summary) gene_patients_occur = out[0] var_patients_occur = out[1] gene_variants_occur = out[2] calculate_occurrence(somatic_summary, gene_patients_occur, var_patients_occur, gene_variants_occur) os.reomve(somatic_summary) # remove intermediate files os.remove(filtered_summary)
def scrape(url): image_page = urllib.request.urlopen(url) image_soup = BeautifulSoup(image_page) for image_link in image_soup.findAll('a'): # print(image_link.get('href')) if "imgsrc" in image_link.get('href') and "jpg" in image_link.get('href'): urllib.request.urlretrieve(image_link.get('href'), "local.jpg") # TODO:mark all the sources in the image # TODO:need a function to put this in the bolb and the DB if random.randint(0,10) > 2: #part of training set link = upload_image(os.getcwd()+"/local.jpg", "comet_trainig") print(link) else: # part of validation set link = upload_image(os.getcwd()+"/local.jpg", "comet_validation") print(link) os.reomve("local.jpg") break
def main(): """\ Usage: sports-naarad [-h] [-F] [-C] live_score|news|[player_stats name] [-my_fav_team] Get latest updates for football and cricket Options: -h, --help shows help(this) message -F, --football [uefa, barclay, fifa] Get football updates. The tournament for which you want to get updates. One of the argumets from uefa, barclay and fifa is compulsory. -C, --cricket Get cricket updates for international matches. [live-score, news, ,fixtures player-stats[name]] Fields to get. `live-scores` to get live socre of on-going matches, `news` to get latest news headlines, `player-stats` to get statistics of player specified. `fixtures` to get updates on upcoming matches. Compulsory single argument. For football option you can give additional options topscorer. Use `-` instead of space in names. --proxy To specify proxy. Defaults to system proxy. Take name of a file. Sample -proxy http://username:password@host:port/ --unset-proxy Removes the proxy set by using --proxy option. """ useage = textwrap.dedent(main.__doc__) args = sys.argv if args[1] == '-h': print(useage) sys.exit(0) try: if '--proxy' in args: with open(sys.path[0] + '/proxy.config', 'w') as f: f.write(args[args.index('-proxy') + 1]) if '--unset-proxy' in args: import os os.reomve(sys.path[0] + '/proxy.config') if args[1] == '-F' or args[1] == '--football' or args[1] == '-f': if '-c' in args or '-C' in args or '--cricket' in args: raise ValueError( 'Both Football and cricket cannot be specified') if args[2] == 'uefa': pass elif args[2].lower() == 'barclay': from sports_naarad.barclay import Barclay if args[3].lower() == 'fixtures': fixture = Barclay().Fixtures(type_return='dict') header = ['Clubs', 'Time(UTC)', 'Location'] print(tabulate(fixture, headers=header, tablefmt='fancy_grid', floatfmt=".2f")) elif args[3].lower() == 'live-score': print('\n'.join(Barclay().liveScore(type_return='dict'))) elif args[3].lower() == 'news': news = Barclay().get_news_headlines(type_return='dict') print() for headline in news: print('Headline: ' + headline + '\n' + 'link: ' + news[headline] + '\n') elif args[3].lower() == 'player-stats': stats = Barclay().playerStats(args[4], type_return='dict') print() for stat in stats: print(stat + ': ' + stats[stat]) elif args[3].lower() == 'topscorer': scorers = Barclay().topScorers(type_return='dict') top_scorers = [] for names in scorers: top_scorers.append((names, scorers[names])) top_scorers = sorted(top_scorers, key=lambda x: int(x[1])) top_scorers.reverse() print(tabulate(top_scorers, headers=[ 'Player Name', 'Goal Scored'], tablefmt='fancy_grid')) else: raise ValueError( 'Not a Valid argument!\n Use -h option for help.') elif args[2] == 'fifa': pass else: raise ValueError( 'Not a Valid argument!\n Use -h option for help') if args[1] == '-C' or args[1] == '-c' or args[1] == '--cricket': from sports_naarad.cricketAPI import Cricket if '-f' in args or '--football' in args: raise ValueError( 'Both Cricket and Football cannot be specifed together!') if args[2].lower() == 'live-score': print(Cricket().live_score(type_return='dict')) elif args[2].lower() == 'fixtures': tournaments = Cricket().list_matches(type_return='dict') header = ['Teams', 'Time and Date', 'Venue', 'Result'] for tournament in tournaments: print("Tournament: {}".format(tournament)) print( tabulate(tournaments[tournament], headers=header, tablefmt='fancy_grid')) print('\n') elif args[2].lower() == 'news': news = Cricket().news(type_return='dict') print() for headline in news: print('Headline: ' + headline + '\n' + 'link: ' + news[headline] + '\n') elif args[2].lower() == 'player-stats': try: stats = Cricket().get_player_stats( args[3], type_return='dict') print('\n') for stat in stats: print(stat + ': ' + stats[stat]) except: raise ValueError('Not a Valid Name!') else: raise ValueError( 'Not a Valid Argument! Use -h or --help for help ') except IndexError: print("Arguments not according to format. Please see help! Use -h option for help")
def __exit__(self, exc_type=None, exc_value=None, exc_tb=None): os.reomve(self.path)