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 using awk or sed, but these only seem to work if the files are unzipped. I would like to edit the files without unzipping them and tried the following code without getting it to work. Thanks.
Using sed:
zcat /dir/* | sed -i~ '2~4s/^.\{6\}//'
Using awk:
zcat /dir/* | awk 'NR%4==2 {gsub(/^....../,"")} 1'
Best Answer
You can't bypass compression, but you can chain the decompress/edit/recompress together in an automated fashion:
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.