Sstrhsrtj

I would like to write a loop to generate 22 R scripts with contents generated in echo. What went wrong in this loop that I could not get the 22 files with the corresponding content?

I tested echo "i want that file" > file.r

It works fine. Then I tested, it treated as two seperate process. First it echo the text, then it generated 22 empty files.

for i in `seq 1 22`; do

    echo "a <- read.delim('file${i}.txt', header=T, check.names=FALSE);

        library('splitstackshape');

        loc1 <- cSplit(a, 'V1', ':');

        rm(a);

        out <- cbind.data.frame(loc1$V1_1, loc1$V1_2);

        write.table(out, 'out_file${i}.txt', sep='t', row.names=F, quote=F)"; 

> build_file${i}.r; done

Then I tried this.. still not working..

    for i in `seq 1 22`; do

    echo "a <- read.delim("file${i}.txt", header=T, check.names=FALSE);

    library("splitstackshape");

    loc1 <- cSplit(a, "V1", ":");

    rm(a);

    out <- cbind.data.frame(loc1$V1_1, loc1$V1_2);

    write.table(out, "out_file${i}.txt", sep="t", row.names=F, quote=F)";

    cat > loc_chr${i}.r; done

Not sure I completely follow the quoting in your script, and what you want the cat command to do, as it reads from the non-redirected stdin, i.e. presumably your keyboard. How about something like

for i in `seq 1 22`

  do cat <<- EOF > loc_chr${i}.r

"a <- read.delim("file${i}.txt", header=T, check.names=FALSE);

    library("splitstackshape");

    loc1 <- cSplit(a, "V1", ":");

    rm(a);

    out <- cbind.data.frame(loc1$V1_1, loc1$V1_2);

    write.table(out, "out_file${i}.txt", sep="t", row.names=F, quote=F)"

EOF

   done

Your first code sample isn't working because it has > build_file${i}.r on it's own line, which is redirecting nothing into 20 files. Append > build_file${i}.r to the end of your echo.

Your second code sample isn't working because of cat at the bottom. You don't supply what you want cat to concatenate, therefore it's waiting for input.

You should delete the cat line, and append > loc_chr${i}.r to the end of your echo.

for i in `seq 1 22`; do

echo "a <- read.delim("file${i}.txt", header=T, check.names=FALSE);

library("splitstackshape");

loc1 <- cSplit(a, "V1", ":");

rm(a);

out <- cbind.data.frame(loc1$V1_1, loc1$V1_2);

write.table(out, "out_file${i}.txt", sep="t", row.names=F, quote=F)" > loc_chr${i}.r

done