Did you try running the logical equivalent of:

Code:

for file in path/to/*.txt ; do
     echo "$file"
     bname=$(basename "$file")
     pref="${bname%%_*.txt}"
     echo "bname: \"$bname\"   pref:\"$pref\""
     # bash /path/to/exon.sh static "$file" > "path/to/${pref}_output.txt"
done

with your actual pathnames and operands, as bakunin suggested? Please show us the output that produced! Like bakunin, I find it hard to believe that pref is being set to the value that I would assume you are trying to set (which isn't at all clear to me).

And, when you run the loop:

Code:

for file in /home/cmccabe/folder/less/*.txt ; do
     bname=$(basename "$file")
     pref="${bname%%_*.txt}"
     set -xv
     /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" \> /home/cmccabe/folder/less/${pref}_output.txt
done
set +xv

(which has the set +xv line after the done instead of before it like bakunin suggested), the whole purpose of enabling tracing on the invocations of exon.sh is so we can all see the trace output produced. But, you haven't shown us any of the trace output???

Please try this slight modification to the above, and show us the output that it produces:

Code:

for file in /home/cmccabe/folder/less/*.txt
do   bname=$(basename "$file")
     pref=${bname%%_*.txt}
     echo "file:\"$file\"    bname:\"$bname\"    pref:\"$pref\""
     echo "output will be directed to:\"/home/cmccabe/folder/less/${pref}_output.txt\""
     #/home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" > "/home/cmccabe/folder/less/${pref}_output.txt"
done

If, and only if, that produces the values that you expect for bname, pref, and the pathname of the file you want to produce, then also try running the following:

Code:

for file in /home/cmccabe/folder/less/*.txt
do   bname=$(basename "$file")
     pref=${bname%%_*.txt}
     #echo "file:\"$file\"    bname:\"$bname\"    pref:\"$pref\""
     #echo "output will be directed to:\"/home/cmccabe/folder/less/${pref}_output.txt\""
     set -xv
     /home/cmccabe/folder/less/exon.sh /home/cmccabe/folder/less/all_cdsV2 "$file" > "/home/cmccabe/folder/less/${pref}_output.txt"
     set +xv
done

and show us the output that produces.

Note that I am not sure why bakunin suggested using \> in the exon.sh command. Doing that makes the redirection operator and the intended output file become operands to exon.sh instead of being a redirection.

I also note that the exon.sh can't be the script that I supplied in post #11. That script didn't look at any of its operands; it only used the presence of one or more operands as a flag to enable debugging printouts. I will assume that you removed the debugging printf statements and the d variable and are using the two operands you are passing to exon.sh as the two filenames processed by that script.