for loop with standard output

Question

I want to run two scripts (gunzip and fastx_collapser) for multiple input files. The output from gunzip should be input to fastx_collapser. How do I do this in a loop function?

My try:

for f in *.gz    gunzip -c "$f"  | fastx_collapser -Q33 -z -o  "${f%}.coll.gz"

Answer 1

You need a do and a done (and some semicolons if you insist on a single line):

for f in *.gz
do
    gunzip -c "$f" | fastx_collapser -Q33 -z -o "${f%}.coll.gz"
done

or:

for f in *.gz; do gunzip -c "$f" | fastx_collapser -Q33 -z -o "${f%}.coll.gz"; done