Alphabet counting


 
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# 1  
Old 01-26-2012
Alphabet counting

I have a text file in the following format
Code:
CCCCCGCCCCCCCCCCcCCCCCCCCCCCCCCC
AAAATAAAAAAAAAAAaAAAAAAAAAAAAAAA
TGTTTTTTTTTTTTGGtTTTTTTTTTTTTTTT
TTTT-TTTTTTTTTCTtTTTTTTTTTTTTTTT

Each row/line will have 32 letters and each line will only have multiple occurrences of 2 letters out of a pool of ATGC (also small atgc). some may have also '-'. I would like to count the occurrence of each alphabet in a line and output the position number/ numbers of the smallest counted alphabet.

Code:
CCCCCGCCCCCCCCCCcCCCCCCCCCCCCCCC  G 7
AAAATAAAAAAAAAAAaAAAAAAAAAAAAAAA   T 5
TGTTTTTTTTTTTTGGtTTTTTTTTTTTTTTT  G 2 15 16
TTTT-TTTTTTTTTCTtTTTTTTTTTTTTTTT    C 15

Please let me know the best way to do it using awk.
Thanks
# 2  
Old 01-27-2012
Have a go with this:

Code:
awk '
    {
        n = split( $0, a, "" );
        for( i = 1; i <= n; i++ )
        {
            count[a[i]]++;
            pos[a[i]] = sprintf( "%s%d ", pos[a[i]], i );
        }

        min = "";
        for( x in count )
        {
            if( match( x, "[ACGT]" ) && (min == "" || count[x] < count[min] ) )
                min = x;
        }

        print $0, min, pos[min];

        delete count;
        delete pos;
    }
' input-file >output-file


Last edited by agama; 01-27-2012 at 12:28 AM.. Reason: better form
This User Gave Thanks to agama For This Post:
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