What do I need to change from my looped unix code to run the perl batch download reference proteomes code from https://www.uniprot.org/help/api_downloading ? I am getting a "zsh: parse error near `done'".
I am also not sure if anything needs to be changed with the perl code or if using the TextEdit application for saving the perl code as .pl was the right approach.
I will be downloading from a list with thousands of taxids in the future. This is a small example I have tried with no success:
cat > taxids.txt 226186 345219 FILE=taxids.txt while read line: do perl apidownload.pl $line done <$FILE