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 = "auto", 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 |
a socket of class connection and sockconn returned by choosebank .Default value (auto) means
that the socket will be set to to the socket component of the banknameSocket variable. |
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 . |
A list with the following components:
bank |
the name of the bank that has been choosen by choosebank.socket |
call |
original call |
name |
list name |
nelem |
number of elements in the list on the server |
typelist |
the type of the elemnts 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 |
J.R. Lobry
citation("seqinr")
## Not run: # Need internet connection # 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) ## End(Not run)