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!")