How to use Bash script to loop through two files

Question

I have a file (file_in.txt) containing these names:

aphid_splitseq.1.fasta.annot.xml
aphid_splitseq.2.fasta.annot.xml
aphid_splitseq.3.fasta.ann         


        

Answer 1

paste can be helpful:

#!/bin/bash

paste file_in.txt file_out.txt | while read if of; do
  echo "-in $if -out $of"
done

yields:

-in aphid_splitseq.1.fasta.annot.xml -out aphid_splitseq_1
-in aphid_splitseq.2.fasta.annot.xml -out aphid_splitseq_2
-in aphid_splitseq.3.fasta.annot.xml -out aphid_splitseq_3
-in aphid_splitseq.4.fasta.annot.xml -out aphid_splitseq_4
-in aphid_splitseq.5.fasta.annot.xml -out aphid_splitseq_5

you can modify this to get the desired behaviour.