Bash loop using two input files as lists

Question

I am trying to optimize a for loop to download files from a website based in a file with SPECIES names and their corresponding numbers of ACCESSION. I want the loop to work first with the first species and the first accession number of the each file and so on... I tried the basic rule but it is not working.

        #!/bin/sh
        #Load modules
        module load sra-toolkit/2.10.7-centos_linux64

Automatized download and assembly of transcritomes. SRA accession and species code required as arguments for the script


        WORKSPACE=/vto
        WORKSPACEFINAL=/vto
        SPECIES=${WORKSPACE}/species_names.txt
        ACCESSION=$accession_numers.txt

        for i in $SPECIES
            for j in $ACCESION
        do
        mkdir $SPECIES
        cd $SPECIES

#SRA download and processing.

        prefetch $ACCESSION

        fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files       ${WORKSPACEFINAL}/ncbi/public/sra/${ACCESSION}.sra -O  ${ACCESSION} 
 

        done

why aren't you using $i and $j inside the loop?

Mheni
– Mheni

2021-01-28 17:52:40 +00:00
Commented Jan 28, 2021 at 17:52 — Mheni
– Mheni, Commented Jan 28, 2021 at 17:52
sorry you are right!!!

VaniT
– VaniT

2021-01-29 16:43:26 +00:00
Commented Jan 29, 2021 at 16:43 — VaniT
– VaniT, Commented Jan 29, 2021 at 16:43

another character escaped · Accepted Answer · 2021-01-29 02:01:29Z

1

Do you have two loops and just one done and do you have that working?
And as @Mheni said it seems that you aren't using the loop's variables
Here an example of a simple script with two loops one inside the other

file_a=$(cat file_a.txt)
file_b=$(cat file_b.txt)

for i in $file_a
do

        for j in $file_b
        do
                printf "$i\n"
                printf "$j\n"
        done
#// if you add code here is outside j loop

done

edited Jan 29, 2021 at 2:01

answered Jan 29, 2021 at 1:55

another character escaped

947 bronze badges

Sign up to request clarification or add additional context in comments.

1 Comment

VaniT Over a year ago

this worked perfectly, thanks specially for the patience with the new ones in programming!

Collectives™ on Stack Overflow

Bash loop using two input files as lists

1 Answer 1

1 Comment

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

1 Comment

Your Answer

Sign up or log in

Post as a guest

Related