How to execute sequential commands un linux

Question

I have what I guess is a pretty basic question about linux. Let us say I have I series of files, which run in couples. Each couple of files is the input of my command, which produces a single output. Then a would like to execute the same command with the following couple, producing a new output.

Let us say, for the example, that I have four files: F1.R1, F1.R2, F2.R1, and F2.R2

My first command would be:

myfunction F1.R1 F1.R2 -output F1

And the second:

myfunction F2.R1 F2.R2 -output F2

I would like to produce a command so that all couples are treated sequentially until all files are processed.

Thanks a lot for your help. Best

Barmar · Accepted Answer · 2023-01-05 21:04:13Z

1

Loop over the .R1 files, replace R1 with R2 to get the other filename from the pair, then execute the command.

for file in *.R1
do
    file2=${file/.R1/.R2}
    output=${file%.R1}
    myfunction "$file" "$file2" --output "$output"
done

answered Jan 5, 2023 at 21:04

Barmar

789k57 gold badges555 silver badges669 bronze badges

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

3 Comments

David R Over a year ago

Hi Barmar, THANKS A LOT. It works for me. I had to tune it a little bit cause *. was giving me trouble, so that I had to use plain *, with no dot. Thanks again.

Barmar Over a year ago

I don't understand that. If the filename is F1.R1 it should be matched by *.R1. Do you have files like F1R1 with no .?

David R Over a year ago

Hi Barmar. I agree, and I did not go deeper into that, because it worked for me without the ".". I will certainly be confronted to a similar situation soon enough, so I'll check it out then.

Collectives™ on Stack Overflow

How to execute sequential commands un linux

1 Answer 1

3 Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

3 Comments

Your Answer

Sign up or log in

Post as a guest

Related