def main(): parser = argparse.ArgumentParser() parser.add_argument( '-update', type=int, default=0, help="update options [#](every # months) , default to manual(0)") args = parser.parse_args() filepath = 'uniprotData/uniprot.txt' dbname = 'uniprot' colname = 'entry' if os.path.exists(filepath): functions.updateMongoDB(filepath, dbname, colname, "1/1/1111") functions.Config_edit(dt.now().date()) if args.update > 0: #train arg set to 1, so for output updated id list functions.setAutoUpdate(args.update) print("Check for update every %s months!" % (args.update)) else: print("File does not exist\n") sys.exit()
def main(): parser = argparse.ArgumentParser() parser.add_argument('-l', help="local filepath", required=True) parser.add_argument('-db', help="database name", required=True) parser.add_argument('-col', help="collection name", required=True) parser.add_argument( '-f', nargs='+', help="features [go,interpro,pfam,prosite,smart,supfam]", required=True) parser.add_argument( '-update', type=int, default=0, help="update options [#](every # months) , default to manual(0)") args = parser.parse_args() filepath = args.l features = { 'go': 0, 'interpro': 0, 'pfam': 0, 'prosite': 0, 'smart': 0, 'supfam': 0 } dbname = args.db colname = args.col if os.path.exists(filepath): if len(args.f) == 1 and args.f[0].lower() == 'all': features = { 'go': 1, 'interpro': 1, 'pfam': 1, 'prosite': 1, 'smart': 1, 'supfam': 1 } else: for i in args.f: features[i.lower()] = 1 functions.updateMongoDB(filepath, features, dbname, colname, "1/1/1111") functions.Config_edit(dt.now().date()) if args.update > 0: #train arg set to 1, so for output updated id list functions.setAutoUpdate(dbname, colname, args.f, 1, args.update) print("Check for update every %s months!" % (args.update)) else: print("File does not exist\n") sys.exit()
def main(): parser = argparse.ArgumentParser() parser.add_argument('-db', help="database name", required=True) parser.add_argument('-col', help="collection name", required=True) parser.add_argument('-f', nargs='+', help="features [go,interpro,pfam,prosite,smart,supfam]", required=True) parser.add_argument('-train', type=int, choices=[0,1],default=0, help="set to 1 for output updated id list,default 0") args = parser.parse_args() features = { 'go' : 0,'interpro' : 0,'pfam' : 0,'prosite' : 0,'smart' : 0,'supfam' : 0 } dbname = args.db colname = args.col train = args.train if len(args.f) == 1 and args.f[0].lower() == 'all': features = {'go' : 1,'interpro' : 1,'pfam' : 1,'prosite' : 1,'smart' : 1,'supfam' : 1} else: for i in args.f: features[i.lower()] = 1 config = configparser.ConfigParser() config.read('config.ini') old_date = dt.strptime(config['DEFAULT']['date'],"%Y-%m-%d") new_date = functions.rssread() if new_date > old_date: getUniprot() if train == 0: functions.updateMongoDB('./uniprotData/uniprot.txt',features,dbname,colname,"1/1/1111") functions.Config_edit(new_date) elif train == 1: functions.updateMongoDB('./uniprotData/uniprot.txt',features,dbname,colname,new_date) functions.Config_edit(new_date) else: print("error") else: print("No new update!")
def main(): parser = argparse.ArgumentParser() parser.add_argument('-train', type=int, choices=[0, 1], default=0, help="set to 1 for output updated id list,default 0") args = parser.parse_args() train = args.train dir_path = os.path.dirname(os.path.realpath(__file__)) config = configparser.ConfigParser() config.read('config.ini') try: old_date = dt.strptime(config['DEFAULT']['date'], "%Y-%m-%d").strftime('%Y-%m-%d') except: print("run setup first!") new_date = functions.rssread() if new_date > old_date: if train == 0: os.system('python ' + dir_path + '/tableGenerator.py') os.system('python ' + dir_path + '/DBtoF.py') os.system('python ' + dir_path + '/annotations.py') subprocess.call( 'makeblastdb -in background_seqs.fasta -dbtype prot -parse_seqids -out mydb', shell=True) functions.Config_edit(new_date) elif train == 1: print("optional?") functions.Config_edit(new_date) else: print("error") else: print("No new update!")
def main(): parser = argparse.ArgumentParser() parser.add_argument( '-l', default='uniprotData/uniprot.txt', help="local filepath,default path can trigger auto download") parser.add_argument( '-update', type=int, default=0, help="update options: check every # months, default to manual(0)") args = parser.parse_args() filepath = args.l ptms = { 'Phosphoserine': [], 'Phosphothreonine': [], 'Phosphotyrosine': [], 'N6-acetyllysine': [], 'Omega-N-methylarginine': [], 'Dimethylated arginine': [], 'Symmetric dimethylarginine': [], 'Asymmetric dimethylarginine': [], 'N6-methyllysine': [], 'N6,N6-dimethyllysine': [], 'N6,N6,N6-trimethyllysine': [], 'N-linked (GlcNAc) asparagine': [], 'S-palmitoyl cysteine': [], 'Pyrrolidone carboxylic acid': [], 'Glycyl lysine isopeptide (Lys-Gly)(interchain with G-Cter in SUMO)': [], 'Glycyl lysine isopeptide (Lys-Gly)(interchain with G-Cter in ubiquitin)': [] } if not os.path.exists("uniprotData"): os.makedirs("uniprotData") if filepath == 'uniprotData/uniprot.txt': functions.getUniprot() if os.path.exists(filepath): tableGeneration(filepath, ptms) if args.update > 0: table_date = functions.rssread() functions.setAutoUpdate(args.update) print("Check for update every %s months!" % (args.update)) functions.Config_edit(table_date) else: print("File does not exist\n") sys.exit()
def main(): parser = argparse.ArgumentParser() parser.add_argument('-train', type=int, choices=[0, 1], default=0, help="set to 1 for output updated id list,default 0") args = parser.parse_args() dbname = "uniprot" colname = "entry" train = args.train config = configparser.ConfigParser() config.read('config.ini') old_date = dt.strptime(config['DEFAULT']['date'], "%Y-%m-%d") new_date = functions.rssread() if new_date > old_date: functions.getUniprot() if train == 0: functions.updateMongoDB('uniprotData/uniprot.txt', dbname, colname, "1/1/1111") functions.Config_edit(new_date) elif train == 1: functions.updateMongoDB('uniprotData/uniprot.txt', dbname, colname, new_date) functions.Config_edit(new_date) else: print("error") dir_path = os.path.dirname(os.path.realpath(__file__)) os.system('python ' + dir_path + '/DBtoF.py') os.system('python ' + dir_path + '/tableGenerator.py') else: print("No new update!")