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[bash] join command

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# 1  
Old 08-17-2009
[bash] join command


I've 2 files:
file 1:
4 3.855143e-07 3.855143e-07
6 1.927572e-07 5.782715e-07
7 3.855143e-07 9.637858e-07
8 1.927572e-07 1.156543e-06
30 4.018987e-05 8.086162e-05

file 2:
1 2.918198e-03 2.918198e-03
2 2.205868e-02 2.497688e-02
3 2.396582e-03 2.737346e-02
4 9.962099e-07 2.737445e-02
7 9.962099e-08 2.737455e-02
30 1.195452e-06 2.737575e-02
31 4.114347e-05 2.741689e-02
I'd like to get an output like:
file output:

4 3.855143e-07 3.855143e-07 9.962099e-07 2.737445e-02
7 3.855143e-07 9.637858e-07 9.962099e-08 2.737455e-02
30 4.018987e-05 8.086162e-05 1.195452e-06 2.737575e-02
if I do like:

join file1 file2

I get
4 3.855143e-07 3.855143e-07 9.962099e-07 2.737445e-02
7 3.855143e-07 9.637858e-07 9.962099e-08 2.737455e-02
Where line 30 miss. I'm reading this old post:
Where a solutionn with awk is suggested.
I mean is possible get the same result with join command?



P.S. if file1 looks like:
4 3.855143e-07 3.855143e-07
6 1.927572e-07 5.782715e-07
7 3.855143e-07 9.637858e-07
30 4.018987e-05 8.086162e-05
the join command work correctly.
# 2  
Old 08-17-2009
Try with awk...

awk 'NR==FNR{arr[$1]?arr[$1]=arr[$1]FS$2FS$3:arr[$1]=$2FS$3}NR!=FNR{ for(i in arr){if(i == $1)print i,arr[i],$2,$3}}' file1 file2

# 3  
Old 08-17-2009
many thanks it works! Smilie

# 4  
Old 08-17-2009
I see you have an awk answer..

wrt the join - if you sort your files before running join it will work - little gotcha :-)

from the man page:

   file1 and file2  must  be  sorted  in  increasing  collating
     sequence  as determined by LC_COLLATE on the fields on which
     they are to be joined, normally the first in each line  (see

And here with your input:

# sort file1
30 4.018987e-05 8.086162e-05
4 3.855143e-07 3.855143e-07
6 1.927572e-07 5.782715e-07
7 3.855143e-07 9.637858e-07
8 1.927572e-07 1.156543e-06

# 5  
Old 08-17-2009
Just of curosity, why was the join command not working, malcomex?? any idea?
# 6  
Old 08-17-2009

about the join command.
I read that Lesser-known Linux commands: join, paste, and sort
the problem is that the 2 files doesn't have a common field. So a solution could be to use the nl tool. (as it suggest).

but i don't understand why if i remove the line 8, it works. there are still line 1, 2 and 6 that don't match.


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