Shell Programming and Scripting

#script foo.sh, calls your script "script.sh" and assumes that #script.sh writes to standard output
while read a
do
        filename=`echo ${a} | cut -d\. -f1`
        echo ${filename}
        ./script.sh ${a} > ${filename}.gff
done

ls [1-9].txt | ./foo.sh

perl genome.gff 1.txt > 1.gff

Replace
 ./script.sh ${a} > ${filename}.gff
with
perl genome.gff ${a} > ${filename}.gff

for FN in *.txt
  do perl genome.gff "$FN" > "${FN%.*}".gff
  done