echo "Co1 Co2 Co3 Co4
A A 1,000 1,000
A B 2,000 1,250
A A 2,000 3,002
A C 2,000 3,005" |awk 'NR==1{print;next}
{a[$1 FS $2]+=gensub(",","",1,$3);b[$1 FS $2]+=gensub(",","",1,$4)}
END{for(i in a) print i,gensub(/(.)(.*)/,"\\1,\\2",1,a),gensub(/(.)(.*)/,"\\1,\\2",1,b)}'
Co1 Co2 Co3 Co4
A A 3,000 4,002
A B 2,000 1,250
A C 2,000 3,005
# cat file
Co1 Co2 Co3 Co4
A A 1,000 1,000
A B 2,000 1,250
A A 2,000 3,002
A C 2,000 3,005
# awk '{$1=$1;gsub(/,/,".")}NR==1{print;next}{a1[$1 OFS $2]+=$3;a2[$1 OFS $2]+=$4}END{for(_ in a1){printf "%s\t%.3f\t%.3f\n",_,a1[_],a2[_]}}' OFS='\t' file
Co1 Co2 Co3 Co4
A A 3.000 4.002
A B 2.000 1.250
A C 2.000 3.005