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How to join, to tsv files, examples:


c   7   r   z
d   6   s   w
f   1   f   f
b   8   p   y
a   9   q   x


a   q   a
c   r   ccc
b   p   bb
0   0   0
d   s   dddd

Here I'd like to "join" them by columns, where a$1,a$3==b$1,b$2 and display rest (a$2,a$4,b$3) :

6   w   dddd
9   x   a
8   y   bb
7   z   ccc

Question is: how would you do this in gawk ?

Order of rows does not metter (in output. In input, order of rows is not defined and can be different in a.tsv and b.tsv - like rows in relational db, they have no order).

Uniqueness note: Originally, I assumed "uniqueness of key={a$1,a$3}. As glenn jackman noticed - it can not be assumed from original problem statement, as it allows not unique rows according to any key - thanks glenn.

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4 Answers 4

up vote 5 down vote accepted

It appears the join command can only join on one field [1,2], so:

awk '
    BEGIN {FS=OFS="\t"}
    NR==FNR {a[$1 FS $3] = $2 FS $4; next}
    $1 FS $2 in a {print a[$1 FS $2], $3}
' a.tsv b.tsv

Update due to comment: since the given key is not unique, here's a technique to build up multiple entries from "a.tsv"

awk '
    BEGIN {FS=OFS="\t"}
    NR==FNR {
        key = $1 FS $3
        if (key in a)
            a[key] = a[key] "\n" $2 FS $4
            a[key] = $2 FS $4
    $1 FS $2 in a {
        split(a[$1 FS $2], ary, /\n/)
        for (idx in ary)
            print ary[idx], $3
' a.tsv b.tsv
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@glenn_jackman I have not been clear enought. Let me be more specific: there are two files, but their filenames can be fixed in sourcecode :). –  Grzegorz Wierzowiecki Oct 24 '11 at 14:59
@glenn_jackman: It is skips records with duplicate keys in a.tsv. It only keeps the last-read one in the array... –  Peter.O Oct 24 '11 at 18:58
@GrzegorzWierzowiecki, answer updated, check it out. –  glenn jackman Oct 24 '11 at 20:45
@glennjackman , Thanks for pointing out uniqueness problem :). –  Grzegorz Wierzowiecki Oct 25 '11 at 8:27

I'd split the task to two different programs:

  1. Use join(1) to join the two files

  2. awk(1) or cut(1) to strip unwanted columns

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JOIN is interesting part. Second - cutting, is clear to me. –  Grzegorz Wierzowiecki Oct 24 '11 at 12:51
join(1). –  sr_ Oct 24 '11 at 12:57
In case I've not stated that clearly enough: There is a UNIX command named join which you may use for that task. –  ktf Oct 24 '11 at 12:58
Thanks, ktf, I haven't knew before about join command, so I misunderstood "join" with question statement. IMHO you were right, and shown clearly that you mean command with brackets, referencing to man page - it was my misunderstood. Thanks again :D. –  Grzegorz Wierzowiecki Oct 28 '11 at 7:40

I don't know awk very well, but it was designed specifically for handling fields in text files, so I presume it can do the job quite well, but because you seemed(?) to express interest in join (in ktf's comments), here is a solution using standard unix tools: join and cut and paste and sort -- lots of "ands", but it works and it might serve as an example of why awk is better :)... I've thown it in mainly for then comparison-of-methods factor.

join -t $'\t' -o 1.2 1.3  2.2  \
 <(paste <(paste <(cut -f1 a.tsv) \
                 <(cut -f3 a.tsv) \
                 | tr '\t' '\0' ) \
         <(cut -f2 a.tsv) \
         <(cut -f4 a.tsv) \
         | sort ) \
 <(paste <(paste <(cut -f1 b.tsv) \
                 <(cut -f2 b.tsv) \
                 | tr '\t' '\0' ) \
         <(cut -f3 b.tsv) \
         | sort ) 
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It's good idea to use combination of sort, cut, paste , as long as we could assume, that both sets have same size and all rows have matching ones. Here you can not assume that, there might be some not matching rows. –  Grzegorz Wierzowiecki Oct 25 '11 at 7:44
@Grzegorz Wierzowiecki: The method above can deal with non matching rows; it does not output them. join handles that... Re file size(rows); again this isn't a problem. paste must have equal numbers of rows, and it gets them if the input is properly delimited... However, on re-visiting this, I noticed a problem caused by concatenating the keys (tr -d '\t'), eg. — X\tXX will match XX\tX as XXX— Fortunately, tr can cope with null chars.. Becaues the null char is not used as a delimiter, the other tools a quite okay with it (I have ammended the answer) –  Peter.O Oct 26 '11 at 15:47
+1 for you fered. I've just read man join. Very nice tool, thanks :). –  Grzegorz Wierzowiecki Oct 26 '11 at 17:26
For general info: To filter out any malformed lines (rows) which don't have the exact number of fields, you can add another filter to each file name. Eg. expecting 4 fields (3 delimiters), this works: <(sed -nr '/^[^\t]*(\t[^\t]*){3}$/p' a.tsv) –  Peter.O Oct 27 '11 at 1:29
In my domain, if any line is malformed, I rise error that whole input has problem. So your tip is good, just to check opposite task: if all lines are correct. Good for readers you've pointed it out, thanks :). –  Grzegorz Wierzowiecki Oct 28 '11 at 7:44

Finally I've managed to do that. So I share my solution :

awk '
    while ((getline < "a.tsv") > 0){
        a2[$1,$3] = $2; a4[$1,$3] = $4
($1,$2) in a2 { print a2[$1,$2] FS a4[$1,$2] FS $3 }' < b.tsv


9   x   a
7   z   ccc
8   y   bb
6   w   dddd

This solution :

  • does not assume order of input rows
  • works, when some rows have no matching in other file
  • assume rows in a.tsv are unique according to key = {a$1,a$3}

For those interested in right join , you just need to delete if( ($1,$2) in a2) statement. For those interested in left join, just do "right join" version and swap a.tsv with b.tsv (and change code accordingly).

Uniqueness note : As glenn jackman noticed, that a.tsv's rows might not be unique according to key={a$1,a$3} , you might like to check out his solution.

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