choosebank {seqinr} | R Documentation

## To select a database structured under ACNUC and located on the web

### Description

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`.

### Usage

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

### Arguments

`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.

### Details

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.

### Value

`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.

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### Note

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

### Author(s)

D. Charif

### References

For more information about the socket communication protocol with ACNUC please get at 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: 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")`

### See Also

`query`, `connection`, `socketConnection`

### Examples

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

[Package seqinr version 1.0-4 Index]