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I am an infrequent user of UNIX, I'm sure this will be fairly trivial for any regular user so I appologize for that. I have the following code:

 for file in /home/sub1/samples/aaa*/*_novoalign.bam
      do
           samtools depth -r chr9:218026635-21994999 *_novoalign.bam < $file > /home/sub2/sub3/${file}.out 
      done

I was hoping the output would be sent to a file in sub2/sub3/ with its name like the input folder. It says 'no file or directory'. I would ideally like to send it here with the '_novoalign.bam' removed and a new ending eg '_output.txt' added. Any tips?

p.s. I don't have permission to write to the directory in which the input file is found.

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I guess the *_novoalign.bam in the samtools call is wrong. –  Hauke Laging Feb 10 at 18:37

2 Answers 2

up vote 0 down vote 
cd /home/sub1/samples
for file in aaa*/*_novoalign.bam; do
    target_file="${file%_novoalign.bam}_output.txt"
    samtools depth -r chr9:218026635-21994999 <"$file" >"$target_file"
done
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up vote 0 down vote

You need to remove the path and then the extension you don't want:

base=${file##*/}
newfile=${base%_novoalign.bam}_output.txt

Then use:

... > "/home/sub2/sub3/$newfile"

Check out Shell Parameter Expansion here for other options:

GNU Bash Documentation

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