open (BC,"file2.txt")||die("cannot open"); open (AB,"file1.txt")||die("cannot open"); @file=; chomp(@file); foreach $fl(@file) { if($fl=~/(.*?)\s+(.*?)\s+(.*?)\s+(.*)/) { $w=$1-1; $x=$2-1; $y=$3-1; $z=$4-1; } while() { @data=split("\t",$_); chomp(@data); push(@col1,$data[$w]); push(@col2,$data[$x]); push(@col3,$data[$y]); push(@col4,$data[$z]); } } for($i=1;$i<@col1;$i++) { if(($col1[$i] eq '+') && ($col2[$i] eq '+') && ($col3[$i] eq '+')) { $j++; } if(($col1[$i] eq '+') && ($col2[$i] eq '+') && ($col4[$i] eq '+')) { $k++; } if(($col3[$i] eq '+') && ($col2[$i] eq '+') && ($col4[$i] eq '+')) { $l++; } if(($col3[$i] eq '+') && ($col2[$i] eq '+') && ($col4[$i] eq '+')&&($col1[$i] eq '+') ) { $m++; } print $col1[0],"\t",$col2[0],"\t",$col3[0],"\t\t",$j,"\n"; print $col1[0],"\t",$col2[0],"\t",$col4[0],"\t\t",$k,"\n"; print $col4[0],"\t",$col2[0],"\t",$col3[0],"\t\t",$l,"\n"; print $col1[0],"\t",$col2[0],"\t",$col3[0],"\t",$col4[0],"\t",$m,"\n"; }