view data_manager/data_manager_eggnog.py @ 2:a74d61dbd155 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/eggnog_mapper commit f431329cd1c7f8a6014207a4ebfd9ffaa67e5497-dirty

#!/usr/bin/env python

from __future__ import print_function

import argparse
import json
import os.path
import sqlite3
from sqlite3 import OperationalError
import sys

def _get_db_version(sqlitedb_path):
    version = '4.5'
    try:
        query = 'select version from version'
        conn = sqlite3.connect(sqlitedb_path)
        cur = conn.cursor()
        cur.execute(query)
        version = cur.fetchone()[0]
    except OperationalError as e:
        print('Assuming eggnog version %s because %s   %s' % (version, sqlitedb_path, e), file=sys.stderr)
    return version

def main():
    parser = argparse.ArgumentParser()
    parser.add_argument( '--config_file' )
    parser.add_argument( '--install_path' )
    parser.add_argument( '--dbs', default='')
    args = parser.parse_args()

    eggnog_db_path = os.path.join(args.install_path,'eggnog.db') 
    if not os.path.exists(eggnog_db_path):
        print('Can not open: %s' % eggnog_db_path, file=sys.stderr)
        exit(1)
    db_version = _get_db_version(eggnog_db_path)

    params = json.loads( open( args.config_file ).read() )
    data_manager_dict = {}
    data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
    data_table = 'eggnog_mapper_db'
    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
    data_table_entry = dict(value=db_version, name=db_version, path=eggnog_db_path)
    data_manager_dict['data_tables'][data_table].append( data_table_entry )
    data_table = 'eggnog_mapper_hmm_dbs'
    data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get( data_table, [] )
    if args.dbs:
        dbs = [x.strip() for x in args.dbs.split(',')]
        for db in dbs:
            key = '%s_%s' % (db_version, db)
            data_table_entry = dict(key=key, db_version=db_version, value=db, name=db, path=db)
            data_manager_dict['data_tables'][data_table].append( data_table_entry )

    # save info to json file
    open( args.config_file, 'wb' ).write( json.dumps( data_manager_dict ) )

if __name__ == "__main__":
    main()