Question

I am using cygwin on Windows 7. I have a folder with about 1200 files of the same type(There are no sub-directories). I am trying to go through the folder and perform a certain action(it’s bioinformatic alignment) on each file. Here is the code that I am using:

$ for file in Project/genomes_0208/*;
do ./bowtie-build $file ../bowtie-0.12.7/indexes/abc;
done


./bowtie – build is the operation that I want to perform. Now, this does complete the operation for all the files in the folder,but it keeps writing the ouput in the same file abc in this case.

So in the end I have only 1 file with the latest output. How can I create 1200 different files , one for each of the input? It doesn’t matter what I name the output files, it could be anything, as long as they are obviously different.

Hope I explained the problem successfully, I’d appreciate any help with this!

Answer 1

How about:

./bowtie-build $file "${file}.out"

If your files had unique names to begin with this should also produce unique output files.