从数据库中检索数据的函数出错

Question

我正在尝试从 NCBI 网站获取 FASTA 文件，我使用以下函数

getncbiseq <- function(accession){
  dbs <- c()
  for (i in 1:numdbs){
    db <- dbs[i]
    choosebank(db)
    resquery <- try(query(".tmpquery", paste("AC=", accession)),silent = TRUE)
    if (!(inherits(resquery, "try-error"))){
      queryname <- "query2"
      thequery <- paste("AC=",accession,sep="")
      query(`queryname`,`thequery`)
      # see if a sequence was retrieved:
      seq <- getSequence(query2$req[[1]])
      closebank()
      return(seq)
    }
    closebank()
  }
  print(paste("ERROR: accession",accession,"was not found"))
}

当我尝试检索序列时

mydata <- getncbiseq("NC_001477")

Error in getSequence(query2$req[[1]]) : object 'query2' not found

还有没有更好的方法来缩短这些循环功能？

如果我使用

query('queryname','the query')
#or 
query("queryname","thequery")

我收到另一个错误

Error in query("queryname", "thequery") : invalid request:"unknown list at (^): \"(^)thequery\""

Answer 1

我认为您打算将对 query() 的调用分配给一个名为 query2 的变量，但您忘记了这样做。试试这个：

if (!(inherits(resquery, "try-error"))) {
  queryname <- "query2"
  thequery <- paste("AC=", accession, sep="")
  query2 <- query(queryname, thequery)
  # see if a sequence was retrieved:
  seq <- getSequence(query2$req[[1]])
  closebank()
  return(seq)
}

正如您所提到的，您的其余代码也有一些可能需要改进的怪癖和问题。

更新：

这是在 dbs 向量上使用 sapply 而不是显式 for 循环（R 人通常不赞成后者）的代码重构：

processdbs <- function(x, y) {
    choosebank(x)
    resquery <- try(query(".tmpquery", paste("AC=", y)), silent = TRUE)
    if (!(inherits(resquery, "try-error"))) {
      queryname <- "query2"
      thequery  <- paste("AC=", y, sep="")
      query2 <- query(queryname, thequery)

      # see if a sequence was retrieved:
      seq <- getSequence(query2$req[[1]])
      closebank()
      return(seq)
    }
    closebank()
}

getncbiseq <- function(accession) {
   dbs <- c("genbank","refseq","refseqViruses","bacterial")
   result <- sapply(dbs, processdbs, y=accession)
   closebank()

   print(paste("ERROR: accession",accession,"was not found"))
}

您可能需要做一些额外的工作来检查 result 向量并确定是否在任何地方检索到序列。

Answer 2

感谢您的大力帮助。我在这一点上被困了一整天。我终于在 windows 10 和 R3.4.0（32 位）下运行了以下代码：-

getncbiseq <- function(accession)
{
require("seqinr") # this function requires the SeqinR R package
# first find which ACNUC database the accession is stored in:
dbs <- c("genbank","refseq","refseqViruses","bacterial")
numdbs <- length(dbs)
for (i in 1:numdbs)
{
db <- dbs[i]
choosebank(db)
# check if the sequence is in ACNUC database 'db':
resquery <- try(query(".tmpquery", paste("AC=", accession)), silent = TRUE)

if (!(inherits(resquery, "try-error"))) {
  queryname <- "query2"
  thequery <- paste("AC=", accession, sep="")
  query2 <- query(queryname, thequery)
  # see if a sequence was retrieved:
  seq <- getSequence(query2$req[[1]])
  closebank()
  return(seq)
}
closebank()
}
print(paste("ERROR: accession",accession,"was not found"))
}

从数据库中检索数据的函数出错

error with a function to retrieve data from a database

r

bioinformatics

ncbi