Re^2: counting the number of 16384 pattern matches in a large DNA sequence (100x faster?)

Replies are listed 'Best First'.
Re^3: counting the number of 16384 pattern matches in a large DNA sequence (100x faster?) by BrowserUk (Patriarch) on Jun 15, 2012 at 15:26 UTC
Did you replace the `...` in `my %seqs = ...;` [download] With your code that loads the hash with your sequences? With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' 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. The start of some sanity?	[reply] [d/l] [select]
Re^3: counting the number of 16384 pattern matches in a large DNA sequence (100x faster?) by BrowserUk (Patriarch) on Jun 15, 2012 at 16:55 UTC
Here is a standalone demonstration that the code I posted works just fine: #! perl -slw use strict; use Time::HiRes qw[ time ]; sub gen{ return @_[1..$#_] if $_[0]==1; map{ my $p=$_; map{ $p . $_ } gen($_[0]-1, @_[1..$#_] ) } @_[1..$#_] } our $N //= 7; my %seqs = map { if( length() ) { my( $id, @seq ) = split "\n", $_; $id => join '', @seq; } else { () } } split '>', do{ local $/; uc( <DATA> ) }; my $start = time; my %counts; for my $seq ( values %seqs ) { ++$counts{ substr $seq, $_, $N } for 0 .. length( $seq ) -$N; } print "Took ", time - $start; print "$_ ::= ", $counts{ $_ } // 0 for gen( $N, qw[A C G T] ); __DATA__ > DNA1 GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCAT TTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTG GAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATT CTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACCTACTA > DNA2 AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAACAATTGAAT GTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGC CAAACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAAT TTTATCTTTAGGCGGTATGCACTTTTAACAGTCACCCCCCAACTAACACA > DNA3 TTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATACAACCCCC GCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAAC CAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAA ATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGC AAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAG > DNA4 AGCATTACTTATATGATATGTCTCCATACCCATTACAATCTCCAGCATTC CCCCTCAAACCTAAGAAATATGTCTGATAAAAGAGTTACTTTGATAGAGT AAATAATAGGAGCTTAAACCCCCTTATTTctaggactatgagaatcgaac ccatccctgagaatccaaaattctccgtgccacctatcacaccccatcct aAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCATACCCCGAAAATGTTG GTTATACCCTTCCCGTACTAATTAATCCCCTGGCCCAACCCGTCATCTAC [download] And some output: `C:\test>976237-2 -N=2 Took 0.000387907028198242 AA ::= 97 AC ::= 86 AG ::= 49 AT ::= 84 CA ::= 99 CC ::= 130 CG ::= 26 CT ::= 71 GA ::= 35 GC ::= 43 GG ::= 27 GT ::= 36 TA ::= 85 TC ::= 68 TG ::= 39 TT ::= 71` [download] With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday' 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. The start of some sanity?	[reply] [d/l] [select]
Re^3: counting the number of 16384 pattern matches in a large DNA sequence (100x faster?) by BrowserUk (Patriarch) on Jun 15, 2012 at 14:42 UTC
Oh sorry. It must be broken.	[reply]