UNIX for Dummies Questions & Answers

1023    A    A    56    0    cc...,,,,..gg..Cc.c,,c..CC..,,
1024    T    T    86    0    ..,,,..aaAA..,,aAA,,a,,A,,a
1025    G    G    125    0    ..,,,,..,,.ttt,,.,.,.TTttT.,.

gawk '{print $1,$2,$3,$4,$6, "\a"length($6)}' text

$ cat data

1023 A A 56 0 ccggCcccCC
1024 T T 86 0 aaAAaAAaAa
1025 G G 125 0 tttTTttT

$ awk '{
        $5=$6;         # Set field 5 to the contents of field 6
        $6=length($5); # Set field 6 to the length of field 5
        NF=6; # Chop off everything after field 6

        # Count the different characters
        for(N=1; N<=length($5); N++) C[substr($5,N,1)]++;
        # Add each different character as a new column, and clear
        # all values in C
        for(X in C) { $(NF+1)=X"="C[X]; delete C[X] }
        print # Print every line
}' data

1023 A A 56 ccggCcccCC 10 C=3 c=5 g=2
1024 T T 86 aaAAaAAaAa 10 A=5 a=5
1025 G G 125 tttTTttT 8 T=3 t=5

$

 
awk '{$5=$6;$6=length($5);NF=6;for(N=1; N<=length($5); N++) C[substr($5,N,1)]++;for(X in C) { $(NF+1)=X"="C[X]; delete C[X] }print}' input.txt

awk 'BEGIN{split("[Aa] [gG] [tT] [cC]",S)}{for(i in S){n=gsub(S[i],x,$6); s=s (s?",":x) S[i]"="n}NF-=1; $5=s; s=x}1' infile

1023 A A 56 [gG]=2,[tT]=0,[cC]=8,[Aa]=0
1024 T T 86 [gG]=0,[tT]=0,[cC]=0,[Aa]=10
1025 G G 125 [gG]=0,[tT]=8,[cC]=0,[Aa]=0