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Full Discussion: Join multiple files by column with awk
Top Forums Shell Programming and Scripting Join multiple files by column with awk Post 302426978 by macsx82 on Thursday 3rd of June 2010 11:31:18 AM
Old 06-03-2010
Join multiple files by column with awk
Hi all,
I searched through the forum but i can't manage to find a solution. I need to join a set of files placed in a directory (~1600) by column, and obtain an output with first and second column common to each file, but following columns are taken from the file in the list (precisely the fourth column of the file). I'll show the input and desired output for more clarity:

File 1:
Code:
name    Chr    Position    Log R Ratio    B Allele Freq
cnvi0000001    5    164388439    -0.4241    0.0097
cnvi0000002    5    165771245    0.4448    1
cnvi0000003    5    165772271    0.4321    0
cnvi0000004    5    166325838    0.0403    0.9971
cnvi0000005    5    166710354    0.2355    0

File 2:
Code:
name    Chr    Position    Log R Ratio    B Allele Freq
cnvi0000001    5    164388439    0.0736    0
cnvi0000002    5    165771245    0.1811    1
cnvi0000003    5    165772271    0.2955    0.0042
cnvi0000004    5    166325838    -0.118    0.9883

File 3:
Code:
name    Chr    Position    Log R Ratio    B Allele Freq
cnvi0000001    5    164388439    0.2449    0
cnvi0000002    5    165771245    -0.0163    1
cnvi0000003    5    165772271    0.3361    0
cnvi0000004    5    166325838    0.0307    0.9867
cnvi0000005    5    166710354    0.1529    0

(note that File 2 has a missing line)

Output:
Code:
chr    Position    File1   File2   File3
5    164388439    -0.4241    0.0736    0.2449
5    165771245    0.4448    0.1811    -0.0163
5    165772271    0.4321    0.2955    0.3361
5    166325838    0.0403    -0.118    0.0307
5    166710354   0.2355                  <tab_separator> 0.1529

Now, I managed to join by column all files using:

Code:
awk '{
   if (x[FNR])
      x[FNR] = sprintf("%s\t%s", x[FNR], $4)
   else
      x[FNR] = $0
}  END {
   for (i=1;i<=FNR;++i)
       print x[i]
}'

but this insert all columns from the first file and next join columns from others files without the insertion of a tab separator or an empty field if there is some file with missing lines, obtaining this (after the manual removal of useless columns):

Output:
Code:
chr    Position    File1   File2   File3
5    164388439    -0.4241    0.0736    0.2449
 5    165771245    0.4448    0.1811    -0.0163
 5    165772271    0.4321    0.2955    0.3361
 5    166325838    0.0403    -0.118    0.0307
 5    166710354   0.2355     0.1529

but as I need this huge file as input to another program, this is not right. now I've tried this solution:

Code:
awk 'NR==FNR{ llr[$1]=$4; p[$1]=$2"\t"$3; next } {
    if(llr[$1]){
        p[$1] = p[$1]"\t"llr[$1]; llr[$1]=$4
    }else{
    llr[$1]="\t";
    p[$1] = p[$1]"\t"llr[$1];
    }      
}
END{for(i in p) {
    print p[i]
}}'

after reading this https://www.unix.com/shell-programmin...ple-files.html

But it doesn't work in the desired way. I have the same output of the first script (but only with useful columns).
I hope I have been clear enough.
If anyone has some ideas, any help will be welcome!
Bye, Macsx

ps. actually I don't matter how the file header is, i can create it by hand.
Last edited by Scott; 09-18-2010 at 05:59 PM.. Reason: More code tags
This User Gave Thanks to macsx82 For This Post:
Danish Shakil
 

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