how to read two input files using sed processing through the bash loop?

Question

Very beginner in bash, already I wrote a small script looping through all the *.txt files and processing the *.txt as an input to a perl script.

Single file as an input

#!/bin/bash
set -e

for i in *.txt
do
  SAMPLE=$(echo ${i} | sed "s/.txt//") 
  echo ${SAMPLE}.txt

time /home/sunn/data/softwares/evaluation/msa/pal2nal.v14/pal2nal.pl ${SAMPLE}.txt -output paml > ${SAMPLE}.paml.txt
done

Actual command for running perl script (2 files as input)

    pal2nal.pl  OG0012884_out.fa OG0012884_out.txt -output paml > OG0012884_paml.txt

Two files as a input ? I got struck..

#!/bin/bash
set -e

for i in *.txt 
do
  SAMPLE=$(echo ${i} | sed "s/.txt//" | "s/.fa//") 
  echo ${SAMPLE}.txt 

time /home/sunn/data/softwares/evaluation/msa/pal2nal.v14/pal2nal.pl ${SAMPLE}.fa ${SAMPLE}.txt -output paml > ${SAMPLE}.paml.txt
done

What's the problem? Please explain what you are trying to do, and how you "got stuck". It helps if you provide example input files and your expected output. — Chris Davies
– Chris Davies, Commented Apr 13, 2021 at 16:09
The perl script needs two input files, *.txt and *.fa. I only loop through only one specific set of files, as subjecting *.txt to a perl script as input. In here, the perl script asks for additional files. How do I show in the bash script ? — Sunny
– Sunny, Commented Apr 13, 2021 at 16:15
Actual command for running perl script , showed in the post. — Sunny
– Sunny, Commented Apr 13, 2021 at 16:17
Yes, I can read your post. I can't guess what you're doing though, which is why I asked for clarification. Please put updates into your question so it's easy for everyone to find and read. — Chris Davies
– Chris Davies, Commented Apr 13, 2021 at 16:21

choroba · Accepted Answer · 2021-04-13 17:12:17Z

3

Just use the variable several times.

You don't need to call sed, parameter expansion can remove the extension, too.

for txt in *_out.txt ; do
    sample=${txt%.txt}
    out=${sample%_out}
    pal2nal.pl "$sample".fa "$sample".txt -output paml > "$out"_paml.txt
done

You might add a check that the other file exists:

    if [[ ! -e $sample.fa ]] ; then
        echo "$sample.fa missing, skipped." >&2
        continue
    fi

edited Apr 13, 2021 at 17:12

answered Apr 13, 2021 at 16:17

choroba

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