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;
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
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