comparison data_manager/FROGS_data_manager.py @ 7:99b2dfb1fa1c draft

planemo upload commit c3ff1475af0e964a0c61458b66e2744c903d8d3d-dirty

6:d11bc4a8f596

    with requests.Session() as s:
        download = s.get(frogs_db_index_link)
        decoded_content = download.content.decode('utf-8')
        db_index = download.content.splitlines()    
        db_index = [line.split("\t") for line in db_index[1:]]
        db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[1]]+[line[4]] for line in db_index]  #add column name

    #get frogs dbs
    dir_name="frogs_db_"+time.strftime("%Y%m%d")
    os.mkdir(dir_name)
    dbs=set([])
    for line in db_index[:2]:
        value=line[4]
        name=value.replace("_"," ")
        link=line[5]

        #download frogs db

        HVL_sources(args.resource)
    elif args.database=="phiX_db_data":
        phiX_sources(args.resource)

    #save info to json file
    filename = args.output
    open(filename, 'wb').write(to_json_string(data_manager_dict))

if __name__ == "__main__":
    main()

7:99b2dfb1fa1c

    with requests.Session() as s:
        download = s.get(frogs_db_index_link)
        decoded_content = download.content.decode('utf-8')
        db_index = download.content.splitlines()    
        db_index = [line.split("\t") for line in db_index[1:]]
        db_index = [line[:4]+[line[1]+"_"+line[2]+"_"+line[3]]+[line[4]] for line in db_index]  #add column name

    #get frogs dbs
    os.chdir(target_directory)
    dir_name="frogs_db_"+time.strftime("%Y%m%d")
    os.mkdir(dir_name)
    dbs=set([])
    for line in db_index:
        value=line[4]
        name=value.replace("_"," ")
        link=line[5]

        #download frogs db

        HVL_sources(args.resource)
    elif args.database=="phiX_db_data":
        phiX_sources(args.resource)

    #save info to json file
    open(filename, 'wb').write(to_json_string(data_manager_dict))

if __name__ == "__main__":
    main()