CODEWITHSUNDEEP
bash
Xizam
Xizam

Reputation: 728

Loading a stdout into a variable in a line using tee

I'm trying to put the amount of lines in a gzipped file in a variable, later on I plan to use this stdout for another process using tee. Why won't the value of wc -l get put into the variable and how can I fix this?

[]$ gzip -dc BC102.fastq.gz | wc -l
4255588
[]$ gzip -dc BC102.fastq.gz | echo $(wc -l)
4255588
[]$ gzip -dc BC102.fastq.gz | reads=$(wc -l); echo $reads
0

The whole line is eventually supposed to look like 

gzip -dc BC102.fastq.gz | tee >(reads=$(wc -l)) | cutadapt -ga...

I don't see how this is a duplicate from How to set a variable to the output from a command in Bash? since I was already applying the answer listed there to echo the value of wc -l directly, but it won't be inserted into the variable.

Upvotes: 2

Views: 1650

Answers (2)

rici
rici

Reputation: 241701

If you set a variable in a subshell, it will have no effect on the parent. That is what happens with

gzip -dc BC102.fastq.gz | tee >(reads=$(wc -l)) | cutadapt -ga...

But nothing obvious stops you from continuing the pipe in the subshell:

reads=$(wc -l <(gzip -dc BC102.fastq.gz | tee >(cutadapt -ga... )))

Upvotes: 2

user5547025
user5547025

Reputation:

tee writes to stdout plus to all files given as arguments. It does not write to two different pipes you could attach to.

Try this:

t=$(tempfile)
reads=$(gzip -dc BC102.fastq.gz | tee $t | wc -l)

Now you can continue in your script

cutadapt -ga $t

while reads contains the number of lines.

Upvotes: 3

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