Question

This question is almost the same as a previous question, but differs enough that the answers for that question don’t work here. Like @chase in the last question, I want to write out multiple files for each split of a dataframe in the following format(custom fasta).

#same df as last question

df <- data.frame(
    var1 = sample(1:10, 6, replace = TRUE)
    , var2 = sample(LETTERS[1:2], 6, replace = TRUE)
    , theday = c(1,1,2,2,3,3)
)    

#how I want the data to look
write(paste(">", df$var1,"_", df$var2, "\n", df$theday, sep=""), file="test.txt")

#whole df output looks like this:
#test.txt
>1_A 
1
>8_A
1
>4_A 
2
>9_A 
2
>2_A 
3
>1_A 
3

However, instead of getting the output from the entire dataframe I want to generate individual files for each subset of data. Using d_ply as follows:

d_ply(df, .(theday), function(x) write(paste(">", df$var1,"_", df$var2, "\n", df$theday, sep=""), file=paste(x$theday,".fasta",sep="")))

I get the following output error:

Error in file(file, ifelse(append, "a", "w")) : 
  invalid 'description' argument
In addition: Warning messages:
1: In if (file == "") file <- stdout() else if (substring(file, 1L,  :
  the condition has length > 1 and only the first element will be used
2: In if (substring(file, 1L, 1L) == "|") { :
  the condition has length > 1 and only the first element will be used

Any suggestions on how to get around this?

Thanks,
zachcp

Answer 1

There were two problems with your code.

• First, in constructing the file name, you passed the vector x$theday to paste(). Since x$theday is taken from a column of a data.frame, it often has more than one element. The error you saw was write() complaining when you passed several file names to its file= argument. Using instead unique(x$theday) ensures that you will only ever paste together a single file name rather than possibly more than one.

• Second, you didn’t get far enough to see it, but you probably want to write the contents of x (the current subset of the data.frame), rather than the entire contents of df to each file.

Here is the corrected code, which appears to work just fine.

d_ply(df, .(theday), 
    function(x) {write(paste(">", x$var1,"_", x$var2, "\n", x$theday, sep=""), 
                       file=paste(unique(x$theday),".fasta",sep=""))
    })