Dear Monks!
I have a file in the following format:
ID:A0AWZ5
HIT:PF12951    SCORE:40.0    EVALUE:2.2e-10    HMM_START:2    HMM_END:
+32    SEQ_START:421    SEQ_END:455
HIT:PF03797    SCORE:130.7    EVALUE:3.6e-40    HMM_START:7    HMM_END
+:261    SEQ_START:822    SEQ_END:1073
HIT:PF12951    SCORE:38.7    EVALUE:5.5e-10    HMM_START:1    HMM_END:
+32    SEQ_START:515    SEQ_END:547
//

[download]

I have generated an array of arrays from this file:
$/="//\n";
while(<>)
{
    if($_=~/^ID:(.*)/m)
    {
        $id=$1;
        $seq=$hash_f{$id};

        @AoA=();
        while($_=~/^HIT:(.*?)\tSCORE:[\d\.]+\tEVALUE:[\d\.\-\w]+\tHMM_
+START:\d+\tHMM_END:\d+\tSEQ_START:(\d+)\tSEQ_END:(\d+)/mg)
        {
            $pfam_name=$1;
            $seq_start=$2;
            $seq_end=$3;

            push @AoA, [ $pfam_name, $seq_start, $seq_end ];
        }
    }

    print $id."\n";
    for $i ( 0 .. $#AoA ) 
    {
        print "$i\t [ @{$AoA[$i]} ],\n";
    }
}
$/="\n";

[download]

which prints:
A0AWZ5
0        [ PF12951 421 455 ],
1        [ PF03797 822 1073 ],
2        [ PF12951 515 547 ],

[download]

My question is the following:
Some of the codes (like PF03797 for example) are different than the rest for the scope of my program. What I need to do is, when I find such codes (I have them stored in a hash), then I would need to find the elements in the array of arrays that are before and after them (if any) and then print the range from the end of the preceding element until the start of the subsequent one.
For example, in the case of A0AWZ5 that I have listed in my example, I would need to print, since PF03797 is indeed one of these "important" codes, the range from 548 (the end of the preceding element in the array of arrays until the end (since there is no subsequent element in this case).

In reply to Stuck in my final step of code using array of arrays by Anonymous Monk

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