awk? adjacency matrix to adjacency list / correlation matrix to list


 
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# 1  
Old 10-01-2011
awk? adjacency matrix to adjacency list / correlation matrix to list

Hi everyone
I am very new at awk but think that that might be the best strategy for this. I have a matrix very similar to a correlation matrix and in practical terms I need to convert it into a list containing the values from the matrix (one value per line) with the first field of the line (row annotation) && the header of the field (column annotation) and some spaces etc. preceding it.
In more abstract terms, I wish to convert an adjacency matrix into adjacency list, which includes the edge weights. In excel it works fine with =IF(B2>0;$A2&" (gg) "&B$1&" = "&B2;"") and some grep but the datasets became just to big. P.S 0 values should be omitted.
Input
 AAABAC...ZZ
AA100.500.7
AB010.300
AC00100.1
...00010
ZZ00001

Output
AA (gg) AA = 1
AA (gg) AC = 0.5
AA (gg) ZZ = 0.7
AB (gg) AB = 1
AB (gg) AC = 0.3
AC (gg) AC = 1
AC (gg) ZZ = 0.1
... (gg) ... = 1
ZZ (gg) ZZ = 1


Thanks a million for your efforts☺.
# 2  
Old 10-01-2011
I've assumed that your input file is a plain ascii file that looks like this:

Code:
         AA     AB      AC      BB      ZZ
AA      1       0       0.5     0       0.7
AB      0       1       0.3     0       0
AC      0       0       1       0       0.1
BB      0       0       0       1       0
ZZ      0       0       0       0       1

columns are tab or space separated. If you want to separate them with some other character that'd work, you'll just need to invoke awk with the -F option that supplies the separator character.

then this small awk programme will generate output like you've indicated:
Code:
#!/usr/bin/env ksh

awk '
    NR == 1 {       # read col headers
        for( i = 1; i <= NF; i++ )
            col_lab[i+1] = $(i);
        next;
    }

    {
        for( i = 2; i <= NF; i++ )
            if( $(i)+0 > 0 )
                printf( "%s (gg) %s  = %s\n", $1, col_lab[i], $(i) );
    }
' input-file-name

I replaced the ... with BB just to have a col/row label. The programme will work with any number of rows/columns. Running the sample file above, yields this output:

Code:
AA (gg) AA  = 1
AA (gg) AC  = 0.5
AA (gg) ZZ  = 0.7
AB (gg) AB  = 1
AB (gg) AC  = 0.3
AC (gg) AC  = 1
AC (gg) ZZ  = 0.1
BB (gg) BB  = 1
ZZ (gg) ZZ  = 1

This User Gave Thanks to agama For This Post:
# 3  
Old 10-02-2011
awk '{if(NR==1){while(i<NF){i++;a[i]=$i;}}else{for(i in a){print a[i]" (gg) "$1" = "$(i+1)}}}' input
This User Gave Thanks to ltomuno For This Post:
# 4  
Old 10-02-2011
Quote:
Originally Posted by ltomuno
awk '{if(NR==1){while(i<NF){i++;a[i]=$i;}}else{for(i in a){print a[i]" (gg) "$1" = "$(i+1)}}}' input
Note that for(i in a) doesn't preserve order, so if column order is important, this is flawed. This also prints columns when the edge value is zero which I believe is undesired as a value of 0 in a correlation matrix indicates no edge in the graph. This also prints as col (gg) row; from the original post this should be reversed.
This User Gave Thanks to agama For This Post:
# 5  
Old 10-02-2011
Using Perl on a space-delimited file:

Code:
$
$
$ cat f11
        AA      AB      AC      BB      ZZ
AA      1       0       0.5     0       0.7
AB      0       1       0.3     0       0
AC      0       0       1       0       0.1
BB      0       0       0       1       0
ZZ      0       0       0       0       1
$
$
$ perl -lane 'if ($.==1){@x=@F} else {for($i=1; $i<=$#F; $i++){print "$F[0] (gg) $x[$i-1] = $F[$i]" if $F[$i] != 0}}' f11
AA (gg) AA = 1
AA (gg) AC = 0.5
AA (gg) ZZ = 0.7
AB (gg) AB = 1
AB (gg) AC = 0.3
AC (gg) AC = 1
AC (gg) ZZ = 0.1
BB (gg) BB = 1
ZZ (gg) ZZ = 1
$
$

tyler_durden
This User Gave Thanks to durden_tyler For This Post:
# 6  
Old 10-02-2011
awk? adjacency matrix to adjacency list / correlation matrix to list

Dear all
Thanks so much for the great solutions. Life is just wonderful if things work as smoothly.
good day to all of you
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