CODEWITHSUNDEEP
awkparallel-processingxargsgnu-parallel
Bamqf
Bamqf

Reputation: 3542

GNU parallel used with xargs and awk

I have two large tab separated files A.tsv and B.tsv, they look like (the header is not in the file): 

A.tsv:  
ID AGE  
User1  18   
...

B.tsv:  
ID INCOME  
User4  49000  
...

I want to select list of IDs in A such that 10=< AGE <=20 and select rows in B that match the list. And I want to use GNU parallel tool. My attempt is two steps:

cat A.tsv | parallel --pipe -q awk '{ if ($3 >= 10 && $3 <= 20) print $1}' > list.tsv

cat list.tsv | parallel --pipe -q xargs -I% awk 'FNR==NR{a[$1];next}($1 in a)' % B.tsv > result.tsv

The first step works but the second one comes with error like: 

awk: cannot open User1 (No such file or directory)

How can I fix this? Does this method work even if A.tsv and list.tsv are 2 to 3 times bigger than the memory?

Upvotes: 4

Views: 2148

Answers (2)

juan4
juan4

Reputation: 1

I know this: (yes, I saw it) GNU parallel used with xargs and awk Asked 8 years, 3 months ago Modified 8 years, 3 months ago Viewed 2k times

My solution: only xargs and awk, only a line without intermediate file, and you don't need install a new tool

awk '{if ($2 >= 10 && $2 <= 20) print $1}' A.tsv | xargs -I myItem awk --assign quebuscar=myItem '$1==quebuscar {print}' B.tsv

Upvotes: 0

user32
user32

Reputation: 177

$ for I in $(seq 8 2 22); do echo -e "User$I\t$I" >> A.txt; done; cat A.txt
User8   8
User10  10
User12  12
User14  14
User16  16
User18  18
User20  20
User22  22

$ for I in $(seq 8 2 22); do echo -e "User$I\t100${I}00" >> B.txt; done; cat B.txt
User8   100800
User10  1001000
User12  1001200
User14  1001400
User16  1001600
User18  1001800
User20  1002000
User22  1002200

$ cat A.txt | parallel --pipe -q awk '{if ($2 >= 10 && $2 <= 20) print $1}' > list.txt
$ cat B.txt | parallel --pipe -q grep -f list.txt
User10  1001000
User12  1001200
User14  1001400
User16  1001600
User18  1001800
User20  1002000

Upvotes: 4

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