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Count and merge using common column

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# 1  
Old 10-31-2012
Count and merge using common column
I have the following records from multiple files.

Code:
415     A       G
415     A       G
415     A       T
415     A       .
415     A       .
421     G       A
421     G       A,C
421     G       A
421     G       A
421     G       A,C
421     G       .
427     A       C
427     A       C
427     A       .
427     A       .

1) i wanted to remove the columns which have "." in third column
2) count the columns and merge based on first column

I want output like this

Code:
 
      3  2,1    415     A       G/T
      5  3,2    421     G       A/A,C
      2         427     A       C

first column "3 2,1 415 A G/T"

3 - how many times 415 is repeated
2,1 - if i count uniq it is giving two times of " 415 A G" and one time "415 A T" pattern. so i wanted to merge this and get final as " 3 2,1 415 G/T"


I used this command to count unique but unable to merge and combine the columns

Code:
cat file | awk '$3 ~/A|T|G|C/{print $0}'| sort | uniq -c

By using above code i am getting the following output

Code:
      2 415     A       G
      1 415     A       T
      3 421     G       A
      2 421     G       A,C
      2 427     A       C

# 2  
Old 10-31-2012
Think this does what you want

Code:
awk '
$3!="." {
    key=$1"\t"$2
    if(!(key in I)) D[++keys]=key
        if(!((key SUBSEP $3) in M)) {
            I[key]++
            K[key,I[key]]=$3
        }
    M[key,$3]++
    S[key]++
}
END {
    for(i=1;i<=keys;i++) {
            key=D[i]
        printf "%d\t", S[key]
        if(I[key]>1)
            for(j=1;j<=I[key];j++)
               printf "%s%d",(j>1?",":""),M[key,K[key,j]]
        printf "\t%s\t", key
        for(j=1;j<=I[key];j++)
               printf "%s%s",(j>1?"/":""),K[key,j]
        printf "\n"
    }
}' infile

This User Gave Thanks to Chubler_XL For This Post:
empyrean
# 3  
Old 11-01-2012
Quote:
Originally Posted by empyrean
Code:
 
      3  2,1    415     A       G/T
      5  3,2    421     G       A/A,C
      2         427     A       C

I assume if second column is count of occurrences. then third row should contain 2 in second column.

This is lit bit nasty code..Smilie

Code:
awk 'function prnt() {
    split(A[S],ARR);
    n=split(ARR[3],ARR_2,"/");
    if(n>1){for(i=1;i<=n;i++){
    var=var?var","UN[ARR[1],ARR[2],ARR_2[i]]:UN[ARR[1],ARR[2],ARR_2[i]]}}
    print CN[S],var,A[S];var=""
    }
    {if($3 != "."){CN[$1]++;if(!UN[$1,$2,$3]++){A[$1]=A[$1]?A[$1]"/"$3:$0;}
    if(S != $1 && S){prnt()}
    {P=$0;S=$1}}}END{prnt()}' OFS="\t" file

This User Gave Thanks to pamu For This Post:
empyrean
# 4  
Old 11-01-2012
@pamu your solution requires that input file is sorted, the solution I posted didn't assume this, mostly because empyrean's posted code required sort:

Code:
cat file | awk '$3 ~/A|T|G|C/{print $0}'| sort | uniq -c

This User Gave Thanks to Chubler_XL For This Post:
empyrean
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