Use zcat and sed or awk to edit compressed .gz text file

Question

I am trying to edit compressed fastq.gz text files, by removing the first six characters of lines 2,6,10,14... I have two different ways of doing this right now, either usin

Answer 1

You can't bypass compression, but you can chain the decompress/edit/recompress together in an automated fashion:

for f in /dir/*; do
  cp "$f" "$f~" &&   
  gzip -cd "$f~" | sed '2~4s/^.\{6\}//' | gzip > "$f"
done

If you're quite confident in the operation, you can remove the backup files by adding rm "$f~" to the end of the loop body.