sorry i got asleep while solving now listen: 
#!/usr/bin/perl
$line=$ARGV[0];  #input file1 containing string list
$name=$ARGV[1];  #output file, given at linux command
chomp($line);
chomp($name);

$amino="ABC";
@cc=split(//,$amino);

    $line=~ s/[\s]//g;
    @prot=split(//,$line);
    $len=@prot;
open(NAS,">>$name"); 
print NAS"0";
close NAS;
open(MAJ,"valfile");  #input file 2 containing values

while($li=<MAJ>){
        chomp($li);
        $val="";
        @value=split(/ +/,$li);

    for($p=0;$p<@prot;$p++){

    for($a=0;$a<@cc;$a++){
        
    
        if($prot[$p] eq "$cc[$a]"){
    
        $val +=$value[$a];
    
        }
    }

    $val1=$val/$len;
    $val1=sprintf "%5.3f",$val1;
    }
    $number++;        
        open(MAL,">>$name");
        print MAL" $number:$val1";
        close MAL;
      
    }
    close MAJ;
    open(MAL1,">>$name");
    print MAL1"\n";
close MAL1;

[download]

this code finely processes the string but only line 1 ;your job is to make it take all lines of string LIKE THE WAY IT TAKES ALL LINES FROM VALUES (input file 2 ) FILE. also go through my original question where instructions/pseudo code is given

In reply to Re^7: string value assignment by abidq
in thread string value assignment by abidq

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