Thanks for the links!

I finished debugging the vast majority of the script at this point, and now I finally have it at a point where it will run to completion without getting stuck in a loop, or encountering an unrecoverable error of some kind.

So, I just ran -d:Dprof, and I am pleased with the output: 

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
 2.10   16.20 16.209    164   0.0988 0.0988  main::GET_TEXT
 0.71   5.460  5.460      1   5.4600 5.4600  main::INDEX_FASTA
 0.40   3.089  3.089    164   0.0188 0.0188  main::ADD_SPAN
 0.15   1.140  1.140      1   1.1400 1.1400  main::WEEDNUM
 0.08   0.599 770.48      2   0.2994 385.24  main::MAIN
 0.05   0.380  0.380      1   0.3800 0.3800  main::OVERLAP
 0.05   0.350  0.350      1   0.3500 0.3500  main::CLUSTER
 0.02   0.130  0.130      2   0.0650 0.0650  main::GET_ENDS
 0.01   0.048  3.176      1   0.0482 3.1764  main::HTML_FORMAT
 0.01   0.040  0.040      1   0.0400 0.0400  main::TABLE_IT
 0.01   0.040  0.420      1   0.0400 0.4200  main::SORT_HITS
 0.00   0.020  0.020      2   0.0100 0.0100  main::WEED_HEADERS
 0.00   0.010  0.010      1   0.0100 0.0100  warnings::BEGIN

[download]
Obviously, a 20 minute run-time is far longer than I would have liked. But 96% of that run-time was in 2 subs. The SEARCHFASTA sub searches a file containing (in this run) a .5 gig file of DNA sequences, searching for every occurance of multiple different strings, and saving them to a large hash. So, in that case, it's going to be dependant on the size of the file being searched, and will be large no matter what I do.

The WEED sub, which is taking 65% of the time, is the one I have to work on then. Its purpose is to organize the results of the SEARCHFASTA sub based on certain criteria, and that is taking it forever. So, I'll have to see what Ican do to tighten that up. I may post that to the Seeking Wisdom node in a bit.

Thanks to everyone for their help and advice. I am taking much of it to heart, and will be keeping a lot of your tips in mind from now on.

Thanks
Matt

In reply to Re^4: Refactoring a large script by mdunnbass
in thread Refactoring a large script by mdunnbass

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