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

I'm slightly confused, because the output doesn't appear to be valid based on the input (homedir different name, directory path different), and when I try the syntax you have, it WFM. Can you double check what you're running and show the exact input/output? — Kenny
– Kenny, Commented Aug 13, 2011 at 21:34
thx. My input comes from two different directory.....Maybe this is the problem? — LookIntoEast
– LookIntoEast, Commented Aug 13, 2011 at 21:37
I'm not sure, tbh. However, I suspect $i doesn't contain what you think it does. Try this, for example: [for i in /tmp/*.tar; do echo $i; done;] If you run that, you get the full path to the files, not just what the * matched. Therefore, it might return '/tmp/foo.tar'. I suspect what you are therefore most likely going to want to do is run some sed/awk magic to strip out just the small part of the file name that you're interested in. — Kenny
– Kenny, Commented Aug 13, 2011 at 21:40

Antti · Accepted Answer · 2011-08-13 21:37:46Z

4

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.

answered Aug 13, 2011 at 21:37

Antti

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2 Comments

LookIntoEast Over a year ago

thanks. it works! I don't fully understand what this 'i' refers to!

Antti Over a year ago

If it helps, you can try it in a shell, by just writing 'for i in *; do echo $i; done'. You'll see that 'i' simply contains the file names as the shell matches them.

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