in reply to Comparing a large set of DNA sequences
This will perform the same job, but run significantly faster (Approx 7 hours).
$| = 1; my $compare_count = 0; for (my $i = 0; $i < @kmers; $i++ ) { for (my $j = $i + 1; $j < @kmers; $j++ ) { my $sims = ( $kmers[ $i ] ^ $kmers[ $j ] ) =~ tr[\0][]; if( $sims == 19 ) { print "Match found: $kmers[ $i ], $kmers[ $j ]"; push @varient_kmers, ($kmers[$i], $kmers[$j]); } ++$compare_count; } } print "\rFinished: $compare_count comparisions made.\n";
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Re^2: Comparing a large set of DNA sequences
by roboticus (Chancellor) on Nov 10, 2011 at 00:24 UTC | |
by aaron_baugher (Curate) on Nov 10, 2011 at 16:17 UTC | |
by roboticus (Chancellor) on Nov 10, 2011 at 16:30 UTC | |
by BrowserUk (Patriarch) on Nov 10, 2011 at 16:26 UTC | |
by roboticus (Chancellor) on Nov 10, 2011 at 18:39 UTC |
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