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( [id://3333]=superdoc: print w/replies, xml ) Need Help??
Late to the party, again, but one thing nobody has commented on is that your if-structure re-tests the same thing multiple times. Instead of:
if (($genome[$i] eq 'a') && ($genome[$i+1] eq 'a')) { ++$tt; } elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 'g')) { ++$a +g; } elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 'c')) { ++$a +c; } elsif (($genome[$i] eq 'a') && ($genome[$i+1] eq 't')) { ++$a +t; } elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'a')) { ++$t +a; } elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'g')) { ++$t +g; } elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 'c')) { ++$g +a; } elsif (($genome[$i] eq 't') && ($genome[$i+1] eq 't')) { ++$t +t; }
you should have had:
if ($genome[$i] eq 'a') { if ($genome[$i+1] eq 'a') { ++$tt; } elsif ($genome[$i+1] eq 'g') { ++$ag; } elsif ($genome[$i+1] eq 'c') { ++$ac; } elsif ($genome[$i+1] eq 't') { ++$at; } } elsif ($genome[$i] eq 't') { if ($genome[$i+1] eq 'a') { ++$ta; } elsif ($genome[$i+1] eq 'g') { ++$tg; } elsif ($genome[$i+1] eq 'c') { ++$ga; } elsif ($genome[$i+1] eq 't') { ++$tt; }
etc.

Of course, the hash is a better solution for this problem, but I thought that the redundant testing problem should be pointed out.


In reply to Re: how can I speed up this perl?? by Roy Johnson
in thread how can I speed up this perl?? by Anonymous Monk

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