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

As long as both your lists are just repetitions of the same kind of name with successive numbers, you shouldn't iterate over files at all. Instead, just count a variable and use that in whatever command you want executed at each step. Example:

COUNT=1
while [ $COUNT -lt 5 ]; do
  mv inputfile$COUNT outputfile$COUNT
  let COUNT++
done

Answer 2

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.

Answer 3

Use While

     While read line 
     do 
       line=$(echo -ne $line | sed or awk)
     done < Directory/filename.t