comment on

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?

In reply to Re^3: counting the number of 16384 pattern matches in a large DNA sequence (100x faster?) by BrowserUk
in thread counting the number of 16384 pattern matches in a large DNA sequence by anonym

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