R中针对不同文件的迭代

Question

我需要一些对我来说有点困难但对于 R 专家程序员来说很容易的东西。我需要使用数据框中包含的信息来迭代我的脚本。 数据框类似于

   pdb       range
1 1a7s_A     78:81
2 1b9o_A     50:53
3 1b9o_A    99:102
4 1bkr_A     27:30
5 1c0p_A 1179:1182
6 1c75_A     42:45

我需要为每一行迭代我的脚本

 pdb <- read.pdb("1a7s_A.pdb") ## here I need to read my pdb file 
    pdb <- atom.select(pdb, resno = 78:81, verbose = T, value = T) ## here I have to put the value in range col

... #my script instruction

table <- data.frame("pdb" = "1a7s_A", ## here I have to insert the name file again 
                    "res" = "78:81",  ## here the range 
                    "omega2" = omega2, "phi2" = phi2,  "psi2" = psi2,
                    "omega3" = omega3, "phi3" = phi3, "psi3" = psi3)

最后，我需要一个包含每个文件迭代的所有信息的 df。

我确定我会将包含所有要读取的文件的目录设置为工作目录。谢谢！

Answer 1

首先，创建一个类似的读取函数

readTableFromRange <- function(tableName,rangeString) {
  filename <- paste0(tableName,".pdb") #get the filename by appendong the pdb-ending
  pdb <- read.pdb(filename)
  rangeNumeric <- eval(parse(text=rangeString)) #getting the range as a numeric vector by evaluating the string as a r-command
  pdb <- atom.select(pdb, resno = rangeNumeric, verbose = T, value = T)
  
  #Enter your script here...
  
  return(data.frame("pdb" = tableName,
                    "res" = rangeString,  
                    "omega2" = omega2, "phi2" = phi2,  "psi2" = psi2,
                    "omega3" = omega3, "phi3" = phi3, "psi3" = psi3))
}

知道你的数据框被称为pa，你可以像这样应用这个函数

tableList <- Map(readTableFromRange,pa$pdb,pa$range)

获取表格列表，最后您可以将它们全部绑定在一起

do.call("rbind",tableList )