run for loop with bash command in fish shell

Question

I'm trying to run a simple command on my fish shell, but I am not able to execute. It just keeps adding lines for me to add additional data to, not sure on how to execute accordingly.

$ for acc in `cat uniprot_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$acc.fasta" ; done > uniprot_seqs.fasta

Answer 1

Fish is not bash compatible, but uses its own scripting language.

In this case the only differences are

1. it doesn't support backticks (```), instead it uses parentheses.
2. for-loops don't use do/done, instead they just end in "end"

for acc in (cat uniprot_ids.txt); curl -s "https://www.uniprot.org/uniprot/$acc.fasta" ; end > uniprot_seqs.fasta

Also command substitutions only split on newlines, not newlines/spaces/tabs, but I'm betting this has entries on lines anyway. If not, you need to use string split.

Answer 2

This might be quite silly of me, using bash command in front of what I actually want to do made this possible:

bash -c 'for acc in `cat meltome_protein_ids.txt` ; do curl -s "https://www.uniprot.org/uniprot/$acc.fasta"; done > uniprot_seqs.fasta'