choosebank              package:seqinr              R Documentation

_T_o _s_e_l_e_c_t _a _d_a_t_a_b_a_s_e _s_t_r_u_c_t_u_r_e_d _u_n_d_e_r _A_C_N_U_C _a_n_d _l_o_c_a_t_e_d _o_n _t_h_e _w_e_b

_D_e_s_c_r_i_p_t_i_o_n:

     This function allows to select one of the databases structured
     under ACNUC and located on the web.  Called without arguments,
     'choosebank()', will return the list of available databases. Then,
     you can use 'query' to make your query and get a list of sequence
     names.  Remote access to ACNUC databases works by opening a socket
     connection on a port (for example  on port number 5558 at
     pbil.univ-lyon1.fr) and by communicating on this socket following
     the protocol  described in the section 'references'.

_U_s_a_g_e:

     choosebank(bank = NA, host = "pbil.univ-lyon1.fr", port = 5558, verbose = FALSE,
                   timeout = 5, infobank = FALSE, tagbank = NA)

_A_r_g_u_m_e_n_t_s:

    bank: String. The name of the bank. If NA, 'choosebank' will return
          the names of all database known by the server.

    host: String. Host name for port

    port: Integer. The TCP port number

 verbose: Logical. If TRUE, verbose mode is on

 timeout: Integer. The timeout in seconds for 'socketConnection'.
          Default 5 seconds.

infobank: Logical. If 'infobank' is TRUE and 'bank' is 'NA', a
          data.frame  with all database informations will be returned

 tagbank: String. If 'bank' is 'NA' and 'tagbank' is documented, the
          names of special purposes databases are returned. Current
          allowed values are TP for frozen databases and TEST for test
          databases. 

_D_e_t_a_i_l_s:

     When called without arguments, 'choosebank()' returns a list of
     all the databases names known  by the server, as a vector of
     string. When called with 'choosebank(infobank = TRUE)', a
     data.frame with more information is returned.

_V_a_l_u_e:

When called with a regular bank name, an (invisible) list with five components: 

  socket: an object of class 'socket' 

bankname: the name of the bank 

 totseqs: the total number of sequences present in the opened database 

totspecs: the total number of species present in the opened database 

 totkeys: the total number of keywords present in the opened database 

When called with bank = NA: 

        : A vector of all available bank names.

When called with bank = NA and infobank = TRUE, a data.frame with three columns: 

    bank: The name of the bank. 

  status: The bank status (on/of). 

    info: Short description of bank with last release date. 

     normal-bracket61bracket-normal

_N_o_t_e:

     The object of class 'socket' will be the first argument of the
     'query' function.

_A_u_t_h_o_r(_s):

     D. Charif

_R_e_f_e_r_e_n_c_e_s:

     For more information about the socket communication protocol with
     ACNUC please get at <URL:
     http://pbil.univ-lyon1.fr/databases/acnuc/remote_acnuc.html>. To
     get the release date and content of all the databases located at
     the pbil, please look at the following url: <URL:
     http://pbil.univ-lyon1.fr/search/releases.php>
      Gouy, M., Milleret, F., Mugnier, C., Jacobzone, M., Gautier,C.
     (1984) ACNUC: a nucleic acid sequence data base and analysis
     system.  _Nucl. Acids Res._, *12*:121-127.
      Gouy, M., Gautier, C., Attimonelli, M., Lanave, C., Di Paola, G.
     (1985)  ACNUC - a portable retrieval system for nucleic acid
     sequence databases: logical and physical designs and usage.
     _Comput. Appl. Biosci._, *3*:167-172.
      Gouy, M., Gautier, C., Milleret, F. (1985) System analysis and
     nucleic acid sequence banks. _Biochimie_, *67*:433-436.

     'citation("seqinr")'

_S_e_e _A_l_s_o:

     'query', 'connection', 'socketConnection'

_E_x_a_m_p_l_e_s:

       ## Not run:  mybank <- choosebank() 
       ## Not run:  choosebank(mybank[1]) 

