parser.add_argument("-a", "--assemblyAccession", required=True)
parser.add_argument("-mdb", "--mongodbname", required=True)
parser.add_argument("-mydbtax", "--mysqldbtaxname", default="bioseqdb")
parser.add_argument("--cpus", default=multiprocessing.cpu_count())
parser.add_argument("-mydbunip", "--mysqldbunip", default="unipmap")
parser.add_argument("-myu", "--mysqldbuser", default="root")
args = parser.parse_args()
args.cpus = int(args.cpus)
mdb = BioMongoDB(args.mongodbname)
tax_db.initialize(
MySQLDatabase(args.mysqldbtaxname,
user=args.mysqldbuser,
passwd=args.dbpass))
ProteinAnnotator.connect_to_db(database=args.mysqldbunip,
user=args.mysqldbuser,
password=args.dbpass)
assert not mdb.seq_col_exists(
args.assemblyAccession), "assembly already exists"
Entrez.email = "*****@*****.**"
assembly_id = Entrez.read(
Entrez.esearch(db="assembly", term=args.assemblyAccession,
retmax=1))["IdList"][0]
resource = Entrez.read(
Entrez.esummary(db="assembly", id=assembly_id, validate=False))
try:
data = resource["DocumentSummarySet"]["DocumentSummary"][0]
name = data["AssemblyName"]
genome = str(data["SpeciesName"])
Entrez.email = "*****@*****.**"
_log = logging.getLogger(__name__)
if __name__ == "__main__":
logger = logging.getLogger('peewee')
logger.setLevel(logging.INFO)
init_log()
mdb = BioMongoDB("saureus")
tax_db.initialize(MySQLDatabase('bioseqdb', user='******', passwd="mito"))
mysql_db.initialize(MySQLDatabase('sndg', user='******', passwd="mito"))
assemblies = list(ExternalAssembly.select().where(
ExternalAssembly.sample_source.is_null(False)))
ProteinAnnotator.connect_to_db(database="unipmap",
user="******",
password="******")
with tqdm(assemblies) as pbar:
for x in pbar:
if mdb.seq_col_exists(x.assembly_accession):
continue
pbar.set_description(x.assembly_accession)
try:
dst_dir = "/data/organismos/" + x.assembly_accession + "/annotation/"
mkdir(dst_dir)
gbpath = x.download_gbk(dst_dir)
from_ref_seq(x.assembly_accession,
gbpath,
tax=x.ncbi_tax,
tmp_dir=dst_dir)
parser.add_argument("-p", "--user_pass", required=True)
parser.add_argument("-dba", "--db_annotation", default="unipmap")
parser.add_argument("-dbu", "--user_db", default="root")
parser.add_argument("-cpu", "--cpu", default="1")
parser.add_argument("-l", "--log_path", default=None)
args = parser.parse_args()
_log = logging.getLogger("protein_annotation")
if not args.log_path:
args.log_path = "/tmp/annotation.log"
init_log(args.log_path, logging.INFO)
pa = ProteinAnnotator()
pa.connect_to_db(database=args.db_annotation,
user=args.user_db,
password=args.user_pass)
BioMongoDB(args.mongo_db, host=args.mdb_host, port=args.mdb_port)
if not os.path.exists(args.blast):
_log.info(args.blast + " does not exists, running blast...")
if args.fasta:
assert os.path.exists(args.fasta), args.fasta + " does not exists"
fasta = args.fasta
else:
_log.info("no fasta input, using proteins from the mongo db")
fasta = tempfile.mktemp()
with open(fasta, "w") as h: