Re^2: Comparing a large set of DNA sequences

[roboticus]

shamshersingh:

Here's what I tried:

#!/usr/bin/perl
use strict;
use warnings;
my %H;
open my $FH, '<', 'DNA_strings.dat' or die $!;
while (<$FH>) {
    s/\s+$//;
    for my $i (0 .. length($_)-1) {
        my $k = $_;
        substr($k,$i,1) = '*';
        push @{$H{$k}}, $_;
    }
}

for my $k (sort keys %H) {
    if ($#{$H{$k}} > 1) {
        print "$k\t", join(",\n\t\t", @{$H{$k}}), "\n";
    }
}

A quick experiment with a short file:

$ cat DNA_strings.dat
CTGAG
CGAGT
ACGCT
TATAC
CTGAA
GGAGC
ATACA
AAAAA
ACAAA
AGAAA
AATAA
AAAGA
ACCAA
AGCAC
CCACG
GCCAT
AGCAA
GGCAT
GTTTG

$ perl DNA_cmp.pl
A*AAA:    AAAAA, ACAAA, AGAAA
A*CAA:    ACCAA, AGCAA
AA*AA:    AAAAA, AATAA
AAA*A:    AAAAA, AAAGA
AC*AA:    ACAAA, ACCAA
AG*AA:    AGAAA, AGCAA
AGCA*:    AGCAC, AGCAA
CTGA*:    CTGAG, CTGAA
G*CAT:    GCCAT, GGCAT

It seems pretty fast, too. It took less than a minute to scan through 100,000 20-character strings, but it didn't find anything. (gen_random_strings.pl is on my my scratchpad)

$ perl gen_random_strings.pl 100000 20 20 ACGT >DNA_strings.dat

$ time perl DNA_cmp.pl

real    0m47.659s
user    0m46.395s
sys     0m1.252s

Update: I tried to make this node a reply to the OP, but for some reason, it kept failing on me, and when I'd refresh, it would show my node replacing BrowserUk's node. It was odd looking...

...roboticus

When your only tool is a hammer, all problems look like your thumb.