Re^2: Increasing the efficiency of a viral clonal expansion model

So you mean change it to this-->

foreach my $nucleotide(@nucleotide_array)
                      {
                          chomp $nucleotide;
                                  
                          my($T,$G,$C,$A);
                          #These mutations rates reflect 10^-5 
                              if ($nucleotide eq 'A'){
                                     # $T=.1;$G=.2;$C=.3;$A=.7;
                                      my $score = (int rand(100000))/1
+00000;
                                      if( $score>=00000 && $score<=.00
+033){ $nucleotide='T';}                       
                                      if( $score>=.000334 && $score<=.
+00066){ $nucleotide='G';} 
                                      if( $score>=.00067 && $score<=.0
+0099){ $nucleotide='C';} 
                                     # if( $score>=.300 && $score<=1.0
+0){  Do NOTHING      } }
                                  }
                              elsif ($nucleotide eq 'T'){
                                     # $A=.1;$G=.2;$C=.3;$T=.7;
                                      my $score = (int rand(100000))/1
+00000;
                                      if( $score>=00000 && $score<=.00
+0333){ $nucleotide='A';}                       
                                      if( $score>=.00034 && $score<=.0
+0066){ $nucleotide='G';} 
                                      if( $score>=.00067 && $score<=.0
+0099){ $nucleotide='C';} 
                                      #if( $score>=.300 && $score<=1.0
+0){  DO NOTHING      } }
                                  }
                              elsif ($nucleotide eq 'C'){
                                     # $T=.1;$G=.2;$A=.3;$C=.7;
                                      my $score = (int rand(100000))/1
+00000;
                                      if( $score>=00000 && $score<=.00
+033){ $nucleotide='T';}                       
                                      if( $score>=.00034 && $score<=.0
+0066){ $nucleotide='G';} 
                                      if( $score>=.00067 && $score<=.0
+0099){ $nucleotide='A';} 
                                      #if( $score>=.300 && $score<=1.0
+0){  #No mutation} 
                                  }
                              elsif ($nucleotide eq 'G'){
                                     # $T=.1;$A=.2;$C=.3;$G=.7;
                                      my $score = (int rand(100000))/1
+00000;
                                      if( $score>=00000 && $score<=.00
+033){ $nucleotide='T';}                       
                                      if( $score>=.00034 && $score<=.0
+0066){ $nucleotide='A';} 
                                      if( $score>=.00067 && $score<=.0
+0099){ $nucleotide='C';} 
                                      #if( $score>=.300 && $score<=1.0
+0){  #No mutation} 
                                  }
                          $new_string= $new_string . $nucleotide;
[download]

Comment on Re^2: Increasing the efficiency of a viral clonal expansion model Download Code

Replies are listed 'Best First'.
Re^3: Increasing the efficiency of a viral clonal expansion model by BrowserUk (Patriarch) on Jul 06, 2011 at 19:27 UTC
Why are you chomping individual characters? `my @nucleotide_array = split //, $seq_string; foreach my $nucleotide ( @nucleotide_array ) { chomp $nucleotide;` [download] It may do no harm to the algorithmm, but calling a function millions of times to do nothing is just silly. Especially when you are concerned with performance. Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply] [d/l]
Re^4: Increasing the efficiency of a viral clonal expansion model by ZWcarp (Beadle) on Jul 06, 2011 at 19:34 UTC
Yeah I suppose you're right. I just type it by habit. Good point!	[reply]
Re^5: Increasing the efficiency of a viral clonal expansion model by BrowserUk (Patriarch) on Jul 06, 2011 at 19:42 UTC
How much memory does the code you posted in the root post use when run with that seed sequence and 120 iterations? And how long does it take to run? Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error. "Science is about questioning the status quo. Questioning authority". In the absence of evidence, opinion is indistinguishable from prejudice.	[reply]
Re^6: Increasing the efficiency of a viral clonal expansion model by ZWcarp (Beadle) on Jul 08, 2011 at 16:31 UTC
Re^7: Increasing the efficiency of a viral clonal expansion model by BrowserUk (Patriarch) on Jul 08, 2011 at 19:15 UTC
Re^3: Increasing the efficiency of a viral clonal expansion model by Anonymous Monk on Jul 06, 2011 at 20:14 UTC
Yes, that is what I mean. Consider this benchmark Read more... (2 kB) And the results Read more... (1445 Bytes) For the length of string in your program (1702) using assignment (SplitAssign ) is faster than using regex (SplitRegex)	[reply] [d/l] [select]