Bash How to execute a command for files in two directories

Question

I know this bash code for execute an operation for all files in one directory:

for files in dir/*.ext; do 
cmd option "${files%.*}.ext" out "${files%.*}.newext"; done

But now I have to execute an operation for all files in one directory with all files in another directory with the same filename but different extension. For example

directory 1 -> file1.txt, file2.txt, file3.txt
directory 2 -> file1.csv, file2.csv, file3.csv

cmd file1.txt file1.csv > file1.newext
cmd file2.txt file2.csv > file2.newext

I must not to compare two files, but the script that I have to execute needs two file to produce another one (in particular I have to execute bwa samsa path_to_ref/ref file1.txt file1.csv > file1.newext)

Could you help me?

Thank you for your answers!

if the count of the files is equal in both directories?

sahaquiel
– sahaquiel

2017-12-27 11:09:35 +00:00
Commented Dec 27, 2017 at 11:09 — sahaquiel
– sahaquiel, Commented Dec 27, 2017 at 11:09

James Brown · Accepted Answer · 2017-12-27 11:40:06Z

1

In bash using variable manipulation:

$ for f in test/* ; do t="${f##*/}";  echo "$f" test2/"${t%.txt}".csv ; done
test/file1.txt test2/file1.csv
test/file2.txt test2/file2.csv
test/file3.txt test2/file3.csv

Edit:

Implementing @DavidC.Rankin's insuring suggestion:

$ touch test/futile
for f in test/*
do 
  t="${f##*/}"
  t="test2/${t%.txt}".csv
  if [ -e "$t" ]
  then 
    echo "$f" "$t"
  fi
done
test/file1.txt test2/file1.csv
test/file2.txt test2/file2.csv
test/file3.txt test2/file3.csv

edited Dec 27, 2017 at 11:40

answered Dec 27, 2017 at 11:11

James Brown

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Comments

pasaba por aqui · Accepted Answer · 2017-12-27 11:18:29Z

0

Try with:

for file in path_to_txt/*.txt; do 
   b=$(basename $file .txt)
   cmd path_to_txt/$b.txt path_to_csv/$b.csv 
done

do not include the paths in call to "cmd" if this command doesn't need them.
"for" statement can not include the path if it is run at directory of .txt files
if execution time is a requisite, you can replace basename by posix regexp. See here https://stackoverflow.com/a/2664746/4886927

edited Dec 27, 2017 at 11:18

answered Dec 27, 2017 at 11:12

pasaba por aqui

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