Bash For Loop with multiple input files of the same name

Question

I am trying to combine a matched set of files with a For loop through a directory of files.

The files look like samename.csfasta and samename.qual, only the extensions are different.

The command to execute the program is:

solid2fastq samename.csfasta samename.qual -o samename

I have been looking for an example online but haven't found one.

if there were only one input:

for f in $FILES
do
     echo "Processing $f file....."
     solid2fastq $f -o $f

done

TIA

i don't understand. what does the input to the script look like? what is $FILES? — Nathan Wallace
– Nathan Wallace, Commented May 29, 2013 at 19:19
So at the beginning of the script I direct it to the folder with the files. FILES=~/folder/folder/* I didn't include that sorry. Using the answer from pipi, I cd into the directory with the files in the script. — Matt Thornton
– Matt Thornton, Commented May 29, 2013 at 19:35

chepner · Accepted Answer · 2013-05-29 19:25:35Z

2

If the files (.cfasta and .qual) are coupled then a code like the following

FILES=( *.csfasta )
for f in "${FILES[@]}"
do
  base=$(basename "$f" .csfasta)
  echo "Processing $f file....."
  solid2fastq "$f" "${base}.qual" -o "$base"
done

should be useful.

edited May 29, 2013 at 19:25

chepner

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answered May 29, 2013 at 19:21

gipi

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