bashfastq

BASH Find Exec Custom Function

I defined the following BASH function to count the number of reads in fastq:

fastq_countGzReads() { zcat "$1" | echo $((`wc -l`/4)) ; }

Now I want to apply this function to a number of gz files found with find.

find . -iname "*gz" -exec sh fastq_countGzReads {} \;


Error:
sh cannot open fastq_countGzReads

How to apply a BASH function on a selection of gz files in a directory ?

Solution

  • A web search on bash find exec function should bring up several hits that cover various ways to slice-n-dice this.

    One idea:

    export -f fastq_countGzReads          # export the function so it can be
                                      # referenced in a follow-on subshell

### and now a tweak to OP's find/-exec

find . -iname "*gz" -exec bash -c 'fastq_countGzReads {}' \;