server.adaptor.execute(sql1, )
server.adaptor.execute(sql2, )
server.adaptor.execute(sql3, )
if __name__ == '__main__':
import argparse
from chlamdb.biosqldb import manipulate_biosqldb
import chlamdb_setup_utils
parser = argparse.ArgumentParser()
parser.add_argument("-i",
'--PMID_sqlite_db',
type=str,
help="input PMID sqlite3 db file")
parser.add_argument("-d",
'--database_name',
type=str,
help="database name")
parser.add_argument("-c",
'--corresp_table',
type=str,
help="hash to locus correspondance table")
args = parser.parse_args()
hash2locus_list = chlamdb_setup_utils.get_hash2locus_list(
args.corresp_table)
load_PMID(args.PMID_sqlite_db, hash2locus_list, args.database_name)
help=
"Tab separated file with correspondance between sequence hashes and locus tags"
)
parser.add_argument("-l",
'--legacy_table',
action="store_true",
help="Create legacy table in biosqldb")
args = parser.parse_args()
biodb = args.database_name
server, db = manipulate_biosqldb.load_db(biodb)
if args.hash2locus_tag:
import chlamdb_setup_utils
hash2locus_list = chlamdb_setup_utils.get_hash2locus_list(
args.hash2locus_tag)
if args.input_interpro:
if not args.legacy_table:
print("creating locus_tag2seqfeature_id")
sql = 'select locus_tag, seqfeature_id from annotation.seqfeature_id2locus_%s' % biodb
locus_tag2seqfeature_id = manipulate_biosqldb.to_dict(
server.adaptor.execute_and_fetchall(sql, ))
print("make table v1")
interpro2biosql(server, hash2locus_list, locus_tag2seqfeature_id,
biodb, *args.input_interpro)
else:
print("creating locus_tag2seqfeature_id")
locus_tag2seqfeature_id = manipulate_biosqldb.locus_tag2seqfeature_id_dict(
server, biodb)
