Re^7: Refactoring a large script

Did you produce a set of timings with the sort factored out of the inner loop, but without the grep?

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Comment on Re^7: Refactoring a large script

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Re^8: Refactoring a large script by mdunnbass (Monk) on Jan 23, 2007 at 16:04 UTC
Not yet, I'll be setting that up this afternoon. You beat me to the punch on that one. I was already planning it. :D Update: Here is the original sub's run times: `Total Elapsed Time = 1135.701 Seconds User+System Time = 770.4718 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 63.8 491.8 491.86 1 491.86 491.86 main::WEED 32.5 251.1 251.10 22012 0.0114 0.0114 main::SEARCHFASTA` [download] And here it is without the switch to grep, but keeping the sorting fixes you suggested, as well as most of your other helps: `Total Elapsed Time = 789.7615 Seconds User+System Time = 741.4615 Seconds Exclusive Times %Time ExclSec CumulS #Calls sec/call Csec/c Name 65.4 485.3 485.35 1 485.35 485.35 main::WEED 33.5 248.8 248.86 22012 0.0113 0.0113 main::SEARCHFASTA 0.96 7.120 7.120 1 7.1200 7.1200 main::INDEX_FASTA` [download] So, removing the double sorting shaved off 6.5 seconds. It's a start.. Now, to try and shave off another 300 or so more.... Matt	[reply] [d/l] [select]

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Re^8: Refactoring a large script
by mdunnbass (Monk) on Jan 23, 2007 at 16:04 UTC

You beat me to the punch on that one. I was already planning it. :D

Update: Here is the original sub's run times:

Total Elapsed Time = 1135.701 Seconds
  User+System Time = 770.4718 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 63.8   491.8 491.86      1   491.86 491.86  main::WEED
 32.5   251.1 251.10  22012   0.0114 0.0114  main::SEARCHFASTA
[download]

And here it is without the switch to grep, but keeping the sorting fixes you suggested, as well as most of your other helps:

Total Elapsed Time = 789.7615 Seconds
  User+System Time = 741.4615 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 65.4   485.3 485.35      1   485.35 485.35  main::WEED
 33.5   248.8 248.86  22012   0.0113 0.0113  main::SEARCHFASTA
 0.96   7.120  7.120      1   7.1200 7.1200  main::INDEX_FASTA
[download]

So, removing the double sorting shaved off 6.5 seconds. It's a start.. Now, to try and shave off another 300 or so more....

Matt

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