The simplest way to speed up your second loop would be to skip over all the non-title lines:


my( $ti, $rt );
{
    {   local $/ = "TITLE="; <MGF>; }
    ( $ti ) = <MGF> =~ m[^(\S+)];
    {   local $/ = "RTINSECONDS="; <MGF> }
    ( $rt ) = <MGF> =~ m[^(\S+)];
    if( exists $IDS{ $ti } ) {
         $IDrtPairs{ $ti } = $rt;
    }
    redo unless eof( MGF );
}

[download]

Warning untested code that probably needs a couple of tweaks, but should explain the idea.

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In reply to Re: Script far too slow with large files - wisdom needed! by BrowserUk
in thread Script far too slow with large files - wisdom needed! by biologistatsea

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