Wow. Just, Wow. The time spent performing the WEED task went from almost 500 seconds down to 33 seconds. Fantastic! 

<b>Urodele 17:47:27</b> ~/Desktop> perl -w weedtest

Benchmark: timing 100000 iterations of mybinary, singlepass, useagrep.
+..
  mybinary:  1 wallclock secs ( 0.58 usr +  0.01 sys =  0.59 CPU) @ 16
+9491.53/s (n=100000)
singlepass:  1 wallclock secs ( 0.58 usr +  0.00 sys =  0.58 CPU) @ 17
+2413.79/s (n=100000)
  useagrep: 270 wallclock secs (266.95 usr +  0.63 sys = 267.58 CPU) @
+ 373.72/s (n=100000)
               Rate   useagrep   mybinary singlepass
useagrep      374/s         --      -100%      -100%
mybinary   169492/s     45253%         --        -2%
singlepass 172414/s     46034%         2%         --

<b>Urodele 17:51:59</b> ~/Desktop> dprofpp

Total Elapsed Time = 361.1940 Seconds
  User+System Time = 306.4840 Seconds
Exclusive Times
%Time ExclSec CumulS #Calls sec/call Csec/c  Name
 80.7   247.5 247.52  22012   0.0112 0.0112  main::SEARCHFASTA
 7.78   23.84 23.849 127206   0.0000 0.0000  main::BANDPASS
 4.45   13.64 13.649    164   0.0832 0.0832  main::GET_TEXT
 3.07   9.399 33.248      1   9.3990 33.248  main::WEED
 2.30   7.060  7.060      1   7.0600 7.0600  main::INDEX_FASTA
 0.82   2.519  2.519    164   0.0154 0.0154  main::ADD_SPAN
 0.60   1.829  4.398      1   1.8292 4.3983  main::HTML_FORMAT
 0.36   1.110  1.110      1   1.1100 1.1100  main::WEEDNUM
 0.20   0.610 308.51      2   0.3049 154.25  main::MAIN
 0.12   0.380  0.380      1   0.3800 0.3800  main::OVERLAP
 0.11   0.340  0.340      1   0.3400 0.3400  main::CLUSTER
 0.05   0.140  0.140      2   0.0700 0.0700  main::GET_ENDS
 0.02   0.050  0.050      1   0.0500 0.0500  main::TABLE_IT
 0.01   0.030  0.410      1   0.0300 0.4100  main::SORT_HITS
 0.01   0.020  0.020      2   0.0100 0.0100  main::WEED_HEADERS

<b>Urodele 17:54:51</b> ~/Desktop>

[download]

Just as a reminder, the dprof output of my original program was:

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]

Thanks!!!

In reply to Re^4: Help tightening up a subroutine please (Updated) by mdunnbass
in thread Help tightening up a subroutine please by mdunnbass

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