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I some directories that contain a similarly named file eg (*Sample_name*.base.coverage.txt). And I would like to paste all of the *base.coverage.txt files together. I have something written, but its not quite right as I don't think I am actually pasting them together. 

cd /g/bo/vir/analysis
find -type d  |
while read dir; do
if [ -f $dir/*.base.coverage.txt ]; then
    paste  $dir/*.base.coverage.txt >> paste_all_l30.p90.base.cov.norm

fi
done

I am also thinking of a different loop method, but I am unsure how to get the list of directories into an array. 

for x in $dir; do cat /$x/*.base.coverage.txt;done > paste_all_l30.p90.base.cov.norm

Any help? thanks

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3 Answers

up vote 0 down vote accepted

try this:

find . -type f -name "*.base.coverage.txt" -exec sh -c 'paste {} paste_all_l30.p90.base.cov.norm > tmp ; mv tmp paste_all_l30.p90.base.cov.norm' \;
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Hmm, snap! (almost) – ams Apr 11 at 12:41
Thanks, but this also just yields a file with one column. – awall Apr 11 at 12:43
Try to change cat to paste like I did in my answer. Is it what you're looking for? – Rush Apr 11 at 12:53
find . -type f -name "*.fastx.allbest.l30.p90.base.cov.norm" -exec paste {} > paste_all_l30.p90.base.cov.norm\ ; find: missing argument to `-exec' – awall Apr 11 at 13:01
That's not going to work anyway because appending to the file is the wrong thing. – ams Apr 11 at 13:04
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up vote 0 down vote

The easiest thing to recurse through a number of directories would be to write a short python script and use the os.path.walk function to recurse through the nested directories. For appending, you could use shutil.copyfileobj within the loop, checking filenames with a regex.

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up vote 1 down vote

Try this:

find . -type f -name '*.base.coverage.txt' \
  | xargs paste > paste_all_l30.p90.base.cov.norm

This will work as long as there are not too many files. If there are a lot of file then this:

touch paste_all_l30.p90.base.cov.norm
for file in `find . -type f -name '*.base.coverage.txt'`; do
  paste paste_all_l30.p90.base.cov.norm $file > tmp
  mv tmp paste_all_l30.p90.base.cov.norm
done
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The OP wants to paste, not cat – Peter.O Apr 11 at 12:48
Ok, I missed that. I've updated the answer – ams Apr 11 at 13:01
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