Hi! I'd like to ask for help because my code isn't behaving correctly (and I can't figure out why). So, here's my issue. I have to deduce positions in a "simple string" given positions in a "complete string". Here's a minimal exemple of my input file: 
#name   complete(cs)    len(cs) simple(ss)  len(ss) pos(cs)
NAME1   A0AAA000AAA00A  14      AAAAAAAA    8        4,6            
NAME2   AAAA0AA00000A   13      AAAAAAA     7        7

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Here's my code: 
$ perl -anle '
    print "$_ position(cs)" and next if /^#/;
    printf "%s",$_;
    for $pos_ss (split ",",$F[5]) {
        $char = substr($F[1],$pos_ss-1,1);
        @cs = split //,$F[3];
        @cs_idx = grep {$cs[$_] eq $char} 0..$#cs;
        push @res,++$cs_idx[$pos_ss-1];
    }
    printf "%14s\n", join ",",@res;
    @res=();
' file

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And here's my expected output: 
NAME1   A0AAA000AAA00A  14      AAAAAAAA    8        4,9    3,5
NAME2   AAAA0AA00000A   13      AAAAAAA     7        7          6

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In the provided exemple, I have to say that the 4th character (which is the 3rd "A") in the complete string(cs) corresponds to the the 3rd character in the simple string(ss), and so on... Could you please help me formatting/reviewing my code? Thanks in advance for your precious help!!

In reply to String processing by dovah

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