| query {seqinr} | R Documentation |
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.
query(listname, query, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
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. |
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://pbil.univ-lyon1.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:
clfcd instead)clfcd instead)clfcd instead)clfcd instead)Operators (always followed and preceded by blanks or parentheses) are:
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.
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 |
Most of the documentation was imported from ACNUC help files written by Manolo Gouy
J.R. Lobry & D. Charif
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")
choosebank,
getSequence,
getName,
crelistfromclientdata
## Not run:
# Need internet connection
choosebank("genbank")
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)