How to assign two variables in a bash for loop script as a pair? [duplicate]

Question

Difficult bash script with the somewhat successful for-loop

#!bin/bash
 
HG19BAM=/3568_5891_5871/3568-NRSA-output-M1chip/3568/3568-hg19-bam 

BW=/3568_5891_5871/3568-NRSA-output-M1chip/3568/3568-hg19-bam/3568-BIGWIG_RPM_tools

source /Users/user/opt/anaconda3/etc/profile.d/conda.sh

VAR1="1 2 3 4 5 6 7 8"

VAR2="39.179 27.394 27.623 32.775 25.2577 30.627 27.6229 30.802"

conda activate Bedtools 
 
for i in $VAR1; do for j in $VAR2
do      
echo "Creating minus strand ${i} scaling to ${j}"

bedtools genomecov -ibam ../3568-MB-${i}.hg19.sorted.F4q10.BLfiltered.bam -bg -scale ${j} -strand - -5 > 3568-${i}.strandminus.5.normRPM.bedGraph

sort -k1,1 -k2,2n 3568-${i}.strandminus.5.normRPM.bedGraph > 3568-${i}.strandminus.5.normRPM.sorted.bedGraph

bedGraphToBigWig 3568-${i}.strandminus.5.normRPM.sorted.bedGraph /Users/user/bin/homer/data/genomes/hg19/chrom.sizes \
     3568-${i}.strandminus.5.normRPM.sorted.bw

echo "Creating positive strand ${i} scaling to ${j}"

bedtools genomecov -ibam ../3568-MB-${i}.hg19.sorted.F4q10.BLfiltered.bam -bg -scale ${j} -strand + -5 > 3568-${i}.strandplus.5.normRPM.bedGraph

sort -k1,1 -k2,2n 3568-${i}.strandplus.5.normRPM.bedGraph > 3568-${i}.strandplus.5.normRPM.sorted.bedGraph

bedGraphToBigWig 3568-${i}.strandplus.5.normRPM.sorted.bedGraph /Users/user/bin/homer/data/genomes/hg19/chrom.sizes \
     3568-${i}.strandplus.5.normRPM.sorted.bw

done
done

conda deactivate

Output:

bash /Users/user/Library/Mobile\ Documents/com\~apple\~TextEdit/Documents/3568-bigiwggenomecov.sh
Creating minus strand 1 scaling to 39.179
Creating positive strand 1 scaling to 39.179
Creating minus strand 1 scaling to 27.394

How do I only pair 1 with 39.179 and 2 with 27.394, etc?

How do I change the for loop so that I do not compare every $VAR1 to every $VAR2?

Note that the linked duplicates are using arrays instead of strings for storing lists. That's proper practice in general: VAR2="39.179 27.394 27.623 32.775 25.2577 30.627 27.6229 30.802" should be var2=( 39.179 27.394 27.623 32.775 25.2577 30.627 27.6229 30.802 ), and then for i in $VAR2 should instead be for i in "${var2[@]}" (if you weren't trying to iterate in lockstep with a second array; since that's the case, you'll want for idx in "${!var2[@]}", and at which point you can refer to "${var2[$idx]}"... or also "${var1[$idx]}") — Charles Duffy
– Charles Duffy, Commented Jul 15, 2022 at 20:25
...see the links up at the top of your question for details. — Charles Duffy
– Charles Duffy, Commented Jul 15, 2022 at 20:26
(use of lower-case variable names is per POSIX recommendation -- see pubs.opengroup.org/onlinepubs/9699919799/basedefs/…; all-caps names are used for variables with meaning to the shell itself and POSIX-defined tools, whereas other names are reserved for application use; your scripts, in this context, are applications -- in reading that spec, keep in mind that environment variables and regular shell variables share a single namespace). — Charles Duffy
– Charles Duffy, Commented Jul 15, 2022 at 20:30

vladtkachuk · Accepted Answer · 2022-07-15 19:33:38Z

0

If you only need pairs, you do not need a nested loop. One of the approaches would be to transform your VAR* into arrays, then you could iterate over let's say i (that is a number of elements in each array) and take VAR1[i] and VAR2[i] in each step.

So you have to find out:

how to transform your input strings to arrays
how to iterate over them at the same time

Hope this gives a correct direction to think about

answered Jul 15, 2022 at 19:33

vladtkachuk

7514 silver badges13 bronze badges

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

1 Comment

Monica B Over a year ago

Thank you! I tried to make an array, but it still did not work :(

Collectives™ on Stack Overflow

How to assign two variables in a bash for loop script as a pair? [duplicate]

1 Answer 1

1 Comment

Linked

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

1 Comment

Linked

Related