Command prompts combination

Question

[K.Gee]

Hello! I have some "weird" txt.files and I found this way to manipulate them.
I use in combination csplit (generates couple of txt files) and join to obtain my desired output. My question is: Is it anyway to combine them in one command?

Im giving you my commands.

csplit -z qrna_ref.txt /AA_QUERY/ {*} -f area.txt  --> generates in this case 4 files named area.txt

join -a1 area.txt00  area.txt01 |join - area.txt02 |join - area.txt03 | join - area.txt04

I tried csplit -z qrna_ref.txt /AA_QUERY/ {*} -f area.txt && join -a1 area.txt00 area.txt01 |join - area.txt02 |join - area.txt03 | join - area.txt04 but it doesnt work...

Thanks in advance!

[Istvan Albert]

It is not clear what you are saying here, the commands do work separately but not when giving the command together?

In what way does it not work?

Do one step at a time, see if you can get it to work - most importantly the files need to be sorted by the field that you join on.

[K.Gee]

Yes exactly. In combination those two commands are not working together. Because the csplit gives an output of 4 files and I was trying to avoid having 4 files as an output and find the way to gave one output file at the end. That was the purpose of my question.

[K.Gee]

Maybe i didn't specify my question. I was trying to avoid having 4 output files at the end, so I was looking if by combining those 2 commands, so as to have one final output instead of 4. But I get your point. So if I understand what your are saying I should try some like: csplit -z qrna_ref.txt /AA_QUERY/ {*} -f area.txt ; cat area.txt00 area.txt01 area.txt02 area.txt03 area.txt04 >out.txt

For having one output file?

Answer 1

[tomc]

'join' is oriented to match columns within a row (as 'join' in relational databases), not to concatenate chunks of rows as you have here. for that use 'cat'

cat area.txt0* > out.txt