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# Generate ID file
sed 's/_length_.*//g' prodigal.tmp.gff > prodigal.id.tmp

# Generate "everything else" file
awk '{print $2, $3, $4, $5, $6, $7, $8, $9}' prodigal.tmp.gff > prodigal.data.tmp

# paste the stuff together
paste prodigal.id.tmp prodigal.data.tmp > prodigal.gff

# Add to the final.gff table
cat prodigal.gff >> final.gff

# clean up the format a bit
sed 's/_v2.6.3//g' final.gff > final.gff.tmp
cat final.gff.tmp | tr ' ' '\t' > final.gff.tmp2
rm final.gff
mv final.gff.tmp2 final.gff