R: To get a list of sequence names from an ACNUC data base...

query {seqinr} | R Documentation

## To get a list of sequence names from an ACNUC data base located on the web

### Description

This is a major command of the package. It executes all sequence retrievals using any selection criteria the data base allows. The sequences are coming from ACNUC data base located on the web and they are transfered by socket. The command produces the list of all sequence names that fit the required criteria. The sequence names belong to the class of sequence `SeqAcnucWeb`.

### Usage

    query(listname, query, socket = autosocket(),
    invisible = TRUE, verbose = FALSE, virtual = FALSE)

### Arguments

`listname` | The name of the list as a quoted string of chars
`query` | A quoted string of chars containing the request with the syntax given in the details section
`socket` | an object of class `sockconn` connecting to a remote ACNUC database (default is a socket to the last opened database).
`invisible` | if `FALSE`, the result is returned visibly.
`verbose` | if `TRUE`, verbose mode is on
`virtual` | if `TRUE`, no attempt is made to retrieve the information about all the elements of the list. In this case, the `req` component of the list is set to `NA`.

### Details

The query language defines several selection criteria and operations between lists of elements matching criteria. It creates mainly lists of sequences, but also lists of species (or, more generally, taxa) and of keywords. See http://doua.prabi.fr/databases/acnuc/cfonctions.html#QUERYLANGUAGE for the last update of the description of the query language.

Selection criteria (no space before the = sign) are:

SP=taxon

  seqs attached to taxon or any other below in tree; @ wildcard possible

TID=id

  seqs attached to given numerical NCBI's taxon id

K=keyword

  seqs attached to keyword or any other below in tree; @ wildcard possible

T=type

  seqs of specified type

J=journalname

  seqs published in journal specified using defined journal code

R=refcode

  seqs from reference specified such as in jcode/volume/page (e.g., JMB/13/5432)

AU=name

  seqs from references having specified author (only last name, no initial)

AC=accessionno

  seqs attached to specified accession number

N=seqname

  seqs of given name (ID or LOCUS); @ wildcard possible

Y=year

  seqs published in specified year; > and < can be used instead of =

O=organelle

  seqs from specified organelle named following defined code (e.g., chloroplast)

M=molecule

  seqs from specified molecule as named in ID or LOCUS annotation records

ST=status

  seqs from specified data class (EMBL) or review level (UniProt)

F=filename

  seqs whose names are in given file, one name per line (unimplemented use `clfcd` instead)

FA=filename

  seqs attached to accession numbers in given file, one number per line (unimplemented use `clfcd` instead)

FK=filename

  produces the list of keywords named in given file, one keyword per line (unimplemented use `clfcd` instead)

FS=filename

  produces the list of species named in given file, one species per line (unimplemented use `clfcd` instead)

listname

  the named list that must have been previously constructed

Operators (always followed and preceded by blanks or parentheses) are:

AND

  intersection of the 2 list operands

OR

  union of the 2 list operands

NOT

  complementation of the single list operand

PAR

  compute the list of parent seqs of members of the single list operand

SUB

  add subsequences of members of the single list operand

PS

  project to species: list of species attached to member sequences of the operand list

PK

  project to keywords: list of keywords attached to member sequences of the operand list

UN

  unproject: list of seqs attached to members of the species or keywords list operand

SD

  compute the list of species placed in the tree below the members of the species list operand

KD

  compute the list of keywords placed in the tree below the members of the keywords list operand

The query language is case insensitive.Three operators (AND, OR, NOT) can be ambiguous because they can also occur within valid criterion values. Such ambiguities can be solved by encapsulating elementary selection criteria between escaped double quotes.

### Value

The result is directly assigned to the object `listname` in the user workspace. This is an objet of class `qaw`, a list with the following 6 components:

`call` | the original call
`name` | the ACNUC list name
`nelem` | the number of elements (for instance sequences) in the ACNUC list
`typelist` | the type of the elements of the list. Could be SQ for a list of sequence names, KW for a list of keywords, SP for a list of species names.
`req` | a list of sequence names that fit the required criteria or `NA` when called with parameter `virtual` is `TRUE`
`socket` | the socket connection that was used

### Note

Most of the documentation was imported from ACNUC help files written by Manolo Gouy

### Author(s)

J.R. Lobry, D. Charif

### References

To get the release date and content of all the databases located at the pbil, please look at the following url: http://doua.prabi.fr/search/releases
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

`choosebank`, `getSequence`, `getName`, `crelistfromclientdata`

### Examples

     ## Not run:
     # Need internet connection
     choosebank("genbank")
     bb <- query("bb", "sp=Borrelia burgdorferi")
     # To get the names of the 4 first sequences:
     sapply(bb$req[1:4], getName)
     # To get the 4 first sequences:
     sapply(bb$req[1:4], getSequence, as.string = TRUE)

    ## End(Not run)

[Package seqinr version 3.4-5 Index]