I don't usually use bash, so I didn't realise this before... seems that the script will work under bash without the typeset -A; have a try and see what happens. I tested it under bash, but didn't notice the complaint about the bad option to typeset.

As for the CRCn issue, I should have suggested this, but thought they were all *1 (I only looked at the first few filenames in your sample, so this is likely my fault). You can use something like this:

Code:

lane_n=${lanename:3:1}   # add this just before the cat command

and when substituting use:

Code:

ColonTrio${lane_n}_

which should take the number from the CRC and append it to ColonTrio.


EDIT: I tested this with bash version 3.2.39 -- if taking away the typeset all together doesn't work, it may be a version difference and another work around will be needed.

---------- Post updated at 15:59 ---------- Previous update was at 15:43 ----------

Here's a solution that should work -- avoids using an associative array in the shell:

Code:

while read old new
do
    eval $old=\"$new\"    # build a list of variables named using old with value that is new. 
done <barcodekey.txt 


find *gz | while IFS="_" read name lanename date sequence lane readpair number
do
    eval xlation=\"\$$sequence\"  # use the old name as a variable to get it's translation.
    if [[ ! -f ColonTrio1_${xlation}_${readpair}.fastq.gz ]]    # not already renamed
    then
        lane_n=${lanename:3:1}    # save the n after CRC
        echo "cat *_${lanename}_*_${sequence}_*_${readpair}* >ColonTrio${lane_n}_${xlation}_${readpair}.fastq.gz"
    fi
done