R/method-download-seq.R

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

## #' @title Retriveing Sequencing from NCBI
## #'
## #' @description
## #' Retriveing sequences from NCBI with the accession ids.
## #' @param ids vector, the accession number or accession.
## #' @param files character, the file name specified by a double-quoted string.
## #' @param databases character, the name of databases to use, default is `protein`,
## #' if nucleotide sequences to retrieve set nuccore,
## #' see also \code{\link[rentrez]{entrez_fetch}}.
## #' @param type character, the format in which to get data,
## #' such as fasta, xml ...,
## #' see also \code{\link[rentrez]{entrez_fetch}}.
## #' @param times integer, the time of sleeping, default is 3, 
## #' meaning 3 seconds.
## #' @param checkids logical, whether check the sequence of 
## #' ids has been retrieved. default is FALSE.
## #' @return the files of sequences downloaded by ids
## #' @importFrom Biostrings readBStringSet
## #' @author Shuangbin Xu
## #' @export
## #' @examples
## #' retrieve_seq(ids=c("ADM52729.1", "AAF82637.1"), 
## #'             files="test.fasta",
## #'             databases="protein",
## #'             type="fasta",
## #'             checkids=TRUE)
## retrieve_seq <- function(ids, files, 
##     databases="protein", 
##     type="fasta", 
##     times=3, checkids=FALSE){
##     if (file.exists(files) && checkids){
##         seqobj <- readBStringSet(files)
##         tmpid <- names(seqobj)
##         tmpid <- unlist(vapply(strsplit(tmpid, " "),function(x){x[1]},character(1)))
##         ids <- setdiff(ids, tmpid)
##     }
##     if (length(ids)>400){
##         stop("The length of ids vector should be shorter than 400!")
##     }
##     if (length(ids)==0){
##         return(NA)
##     }
##     cat(ids)
##     cat("\n")
##     tryCatch({tmprecs <- rentrez::entrez_fetch(db=databases, ids, rettype=type)
##               tmprecs <- gsub("\n\n", "\n", tmprecs)
##               #tmprecs <- str_trim(tmprecs)
##               tmprecs <- substr(tmprecs, 1, nchar(tmprecs)-1)
##               write(tmprecs, files, append=TRUE)
##     },error=function(e){do.call("retrieve_seq", 
##                         args=list(ids=ids, databases=databases, 
##                                   type=type, files=files, checkids=TRUE))})
##     message(paste0("Sleeping ... ",times,"s"))
##     Sys.sleep(times)
## }
## 
## #' @title Retriveing Sequencing from NCBI By mapply
## #'
## #' @description
## #' Retriveing sequences from NCBI with the accession ids.
## #' @param idlist vector, the accession version.
## #' @param files character, the file name specified by a double-quoted string.
## #' @param databases character, the name of databases to use, default is `protein`,
## #' if nucleotide sequences to retrieve set nuccore,see \code{\link[rentrez]{entrez_fetch}}.
## #' @param type character, the format in which to get data,such as fasta, xml ...,
## #' see \code{\link[rentrez]{entrez_fetch}}.
## #' @param times integer, the time of sleeping, default is 3, 
## #' meaning 3 seconds.
## #' @param checkids logical, whether check the sequence of ids has been retrieved.
## #' default is FALSE.
## #' @return the files of sequences downloaded by ids
## #' @seealso \code{\link[MicrobiotaProcess]{retrieve_seq}}
## #' @author Shuangbin Xu
## #' @export
## #' @examples
## #' idslist <- list(c("ADM52729.1", "AAF82637.1"), 
## #'                 c("CAA24729.1", "CAA83510.1"))
## #' mapply_retrieve_seq(idlist=idslist,
## #'                   files="test.fasta",
## #'                   databases="protein",
## #'                   type="fasta",
## #'                   times=3,checkids=TRUE)
## mapply_retrieve_seq <- function(idlist, files, 
##     databases="protein", 
##     type="fasta", 
##     times=3, checkids=TRUE){
##     invisible(mapply(retrieve_seq, 
##                      idlist, 
##                      MoreArgs=list(files=files,
##                                    databases=databases,
##                                    type=type,
##                                    times=times,
##                                    checkids=checkids),
##                      SIMPLIFY=FALSE))
## }