bash for command

Question

#!/bin/bash

for i in /home/xxx/sge_jobs_output/split_rCEU_results/*.rCEU.bed
do
intersectBed -a /home/xxx/sge_jobs_output/split_rCEU_results/$i.rCEU.bed -b /home/xxx/sge_jobs_output/split_NA12878_results/$i.NA12878.bed -f 0.90 -r > $i.overlap_90.bed
done

However I got the errors like:

Error: can't determine file type of '/home/xug/sge_jobs_output/split_NA12878_results//home/xug/sge_jobs_output/split_rCEU_results/chr4.rCEU.bed.NA12878.bed': No such file or directory

Seems the computer mixes the two .bed files together, and I don't know why. thx

Answer 1

Your i has the format /home/xxx/sge_jobs_output/split_rCEU_results/whatever.rCEU.bed, and you insert it to the file name, which leads to the duplication. It's probably simplest to switch to the directory and use basename, like this:

pushd /home/xxx/sge_jobs_output/split_rCEU_results
for i in *.rCEU.bed
do
    intersectBed -a $i -b ../../sge_jobs_output/split_NA12878_results/`basename $i .rCEU.bed`.NA12878.bed -f 0.90 -r > `basename $i .NA12878.bed`.overlap_90.bed
done
popd

Notice the use of basename, with which you can replace the extension of a file: If you have a file called filename.foo.bar, basename filename.foo.bar .foo.bar returns just filename.