mysql_user,
mysql_pwd,
mysql_db,
main_blastnr_table=True,
alternate_tables=True)
if args.load_tables:
server, db = manipulate_biosqldb.load_db(biodb)
sys.stdout.write("creating locus_tag2seqfeature_id")
locus_tag2seqfeature_id = manipulate_biosqldb.locus_tag2seqfeature_id_dict(
server, biodb)
sys.stdout.write("creating protein_id2seqfeature_id")
protein_id2seqfeature_id = manipulate_biosqldb.protein_id2seqfeature_id_dict(
server, biodb)
sys.stdout.write("getting seqfeature_id2locus_tag")
seqfeature_id2locus_tag = manipulate_biosqldb.seqfeature_id2locus_tag_dico(
server, biodb)
sys.stdout.write("getting locus_tag2accession")
locus_tag2accession = manipulate_biosqldb.locus_tag2accession(
server, args.mysql_database)
blastnr2biosql(seqfeature_id2locus_tag, locus_tag2seqfeature_id,
protein_id2seqfeature_id, locus_tag2accession, biodb,
args.n_procs, mysql_host, mysql_user, mysql_pwd,
mysql_db, *args.input_blast)
print("creating orthology table")
print("number of groups", len(orthogroup2detailed_count))
create_orthology_mysql_table(server, orthogroup2detailed_count,
args.db_name)
print("get locus_tag2taxon_id dictionnary...")
locus_tag2genome_taxon_id = manipulate_biosqldb.locus_tag2genome_taxon_id(
server, args.db_name)
print('creating locustag2seqfature_id table')
get_locus2seqfeature_table.create_locus_tag2seqfeature_table(
args.db_name, locus_tag2seqfeature_id, locus_tag2genome_taxon_id)
print("get protein_id2seqfeature_id")
protein_id2seqfeature_id = manipulate_biosqldb.protein_id2seqfeature_id_dict(
server, args.db_name)
print("get locus_tag2accession dictionnary...")
locus_tag2accession = manipulate_biosqldb.locus_tag2accession(
server, args.db_name)
print("get protein_id2accession dictionnary...")
protein_id2accession = manipulate_biosqldb.protein_id2accession(
server, args.db_name)
print("getting location")
seqfeature_id2seqfeature_location = manipulate_biosqldb.seqfeature_id2feature_location_dico(
server, args.db_name)
print("getting seqfeature_id2protein_id")
seqfeature_id2protein_id = manipulate_biosqldb.seqfeature_id2protein_id_dico(