def main(argv=None): # IGNORE:C0111
program_version = "v%s" % __version__
program_build_date = str(__updated__)
program_version_message = '%%(prog)s %s (%s)' % (program_version,
program_build_date)
program_shortdesc = __import__('__main__').__doc__.split("\n")[1]
program_license = '''%s
Created by user_name on %s.
Copyright 2015 BIA. All rights reserved.
Licensed under the Apache License 2.0
http://www.apache.org/licenses/LICENSE-2.0
Distributed on an "AS IS" basis without warranties
or conditions of any kind, either express or implied.
USAGE
''' % (program_shortdesc, str(__date__))
parser = ArgumentParser(description=program_license,
formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-v",
"--verbose",
dest="verbose",
action="count",
help="set verbosity level [default: %(default)s]")
parser.add_argument("-db_structure",
"--db_structure",
help="Mongo structure db",
default='pdb')
parser.add_argument("-db_genome",
"--db_genome",
help="Mongo proteins db",
default='saureus')
parser.add_argument('-o', '--overwrite', default=True, action='store_true')
parser.add_argument("-host", "--db_host", default='127.0.0.1')
parser.add_argument('-V',
'--version',
action='version',
version=program_version_message)
args = parser.parse_args()
db = pymongo.MongoClient(args.db_host)[args.db_structure]
BioMongoDB(args.db_genome)
logging.getLogger("peewee").setLevel(logging.WARN)
from peewee import MySQLDatabase
from SNDG.BioMongo.Process.Taxon import tax_db
tax_db.initialize(MySQLDatabase('bioseqdb', user='******', passwd="mito"))
tax_cache = {}
for t in Taxonomy.objects().no_cache():
for n in t.names:
tax_cache[n.lower()] = t
tax_cache[t.ncbi_taxon_id] = t
query = {}
idx_name = "sndg_index"
if not args.overwrite:
query = {idx_name: {"$exists": 0}}
# total = db.structures.count(query)
# with tqdm(db.structures.find(query, {"organism": 1}), total=total) as pbar:
# for struct in pbar:
# if "organism" in struct:
# for org in [x for x in set(struct["organism"].lower().split(";") + struct["organism"].lower().split(",") +
# [struct["organism"].lower().split("(")[0]]) if ";" not in x and "," not in x and "(" not in x]:
# org = org.strip()
# val = get_or_load_by_name(org, tax_cache)
# if val:
# db.structures.update({"_id": struct["_id"]}, {"$set": {idx_name + ".tax": list(val.keywords)}})
# else:
# tax_cache[org.lower()] = None
# _log.warn(org + " not found")
# db.structures.update({"ligands.0":{"$exists",1}}, {"$set": {idx_name + ".ligand": 1}},multi=True);
db = pymongo.MongoClient(args.db_host)[args.db_genome]
# total = db.barcodes.count(query)
# with tqdm(db.barcodes.find(query, {"tax": 1}), total=total) as pbar:
# for barcode in pbar:
# val = get_or_load_by_id(barcode["tax"], tax_cache)
# update_element(val, db.barcodes, barcode, idx_name, tax_cache,barcode["tax"])
total = db.sequence_collection.count(query)
with tqdm(db.sequence_collection.find(query, {
"name": 1,
"tax": 1,
"assemblyStatus": 1
},
no_cursor_timeout=True),
total=total) as pbar:
for genome in pbar:
if "tax" in genome:
val = get_or_load_by_id(int(genome["tax"]["tid"]), tax_cache)
update_element(val, db.sequence_collection, genome, idx_name,
tax_cache, genome["tax"]["tid"])
if val:
select = {"organism": genome["name"]}
kws = list(val.keywords)
db.proteins.update(select,
{"$set": {
idx_name + ".tax": kws
}},
multi=True)
db.proteins.update(
select, {"$addToSet": {
"keywords": {
"$each": kws
}
}},
multi=True)
db.contig_collection.update(select, {
"$set": {
idx_name + ".tax": kws,
idx_name + ".assemblyStatus":
genome["assemblyStatus"]
}
},
multi=True)
db.contig_collection.update(
select, {"$addToSet": {
"keywords": {
"$each": kws
}
}},
multi=True)
print("Ok")
sf.qualifiers["locus_tag"] = [
x.id + "_" +
sf.qualifiers["locus_tag"][0].replace(tag, "")
]
contigs.append(x)
GFF.write(contigs, h, False)
if __name__ == '__main__':
init_log()
logging.getLogger("peewee").setLevel(logging.WARN)
from peewee import MySQLDatabase
from SNDG.BioMongo.Process.Taxon import tax_db
tax_db.initialize(MySQLDatabase('bioseqdb', user='******', passwd="mito"))
mdb = BioMongoDB("saureus", port=27017)
# mdb.delete_seq_collection("ILEX_PARA2")
def extract_annotation_feature(feature):
mrnas = [f for f in feature.sub_features if f.type == "mRNA"]
return mrnas[0] if feature.type == "gene" and len(mrnas) else feature
def accept_protein_feature(feature):
return feature.type == "gene" and feature.sub_features and feature.sub_features[
0].type == "mRNA"
# prot_dict = bpio.to_dict(bpio.parse("/data/organismos/ILEX_PARA/contigs/ncbi_IP4.faa","fasta"))
def extract_sequence(c, f):
init_log()
parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-p", "--dbpass", required=True)
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: