| crelistfromclientdata {seqinr} | R Documentation |
This function is usefull if you have a local file with sequence names (sequence ID), or sequence accession numbers, or species names, or keywords. This allows you to create on the server a list with the corresponding items.
crelistfromclientdata(listname, file, type, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE) clfcd(listname, file, type, socket = autosocket(), invisible = TRUE, verbose = FALSE, virtual = FALSE)
listname |
The name of the list as a quoted string of chars |
file |
The local file name |
type |
Could be one of "SQ", "AC", "SP", "KW", see examples |
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. |
clfcd is a shortcut for crelistfromclientdata.
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 |
J.R. Lobry
citation("seqinr")
choosebank,
query, savelist for the reverse operation with
an ACNUC list of sequences.
## Not run:
# Need internet connection
choosebank("emblTP")
#
# Example with a file that contains sequence names:
#
fileSQ <- system.file("sequences/bb.mne", package = "seqinr")
crelistfromclientdata("listSQ", file = fileSQ, type = "SQ")
sapply(listSQ$req, getName)
#
# Example with a file that contains sequence accession numbers:
#
fileAC <- system.file("sequences/bb.acc", package = "seqinr")
crelistfromclientdata("listAC", file = fileAC, type = "AC")
sapply(listAC$req, getName)
#
# Example with a file that contains species names:
#
fileSP <- system.file("sequences/bb.sp", package = "seqinr")
crelistfromclientdata("listSP", file = fileSP, type = "SP")
sapply(listSP$req, getName)
#
# Example with a file that contains keywords:
#
fileKW <- system.file("sequences/bb.kwd", package = "seqinr")
crelistfromclientdata("listKW", file = fileKW, type = "KW")
sapply(listKW$req, getName)
#
# Summary of ACNUC lists:
#
sapply(alr()$rank, getliststate)
closebank()
## End(Not run)