Wait ... you mean your proteins are not single letters? But actually a 9 digit number like 648040620? Then the regex solution as mentioned above will not work and I think you better put your data in arrays and use List::Compare to calculate the set intersection and such.
CountZero A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James
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[d/l] |
I like the List::Compare. It looks good. I'm just worried about, because my array will be at least 5 million in length.
Can you offer me any peace of mind?
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Here is some code which does what you want:
use Modern::Perl;
use List::Compare;
# Make two arrays with fake data
my @left = map {'AA' . int(rand (5000000) + 1000000)} (1 ... 5000000)
+;
my @right = map {'AA' . int(rand (5000000) + 1000000)} (1 ... 5000000)
+;
my $start = time;
my $lc = List::Compare->new('-u', \@left, \@right);
{
open my $OUT_INTER, '>', './intersection.txt';
say $OUT_INTER $_ for $lc->get_intersection;
}
{
open my $OUT_DIFF, '>', './difference.txt';
say $OUT_DIFF $_ for $lc->get_symmetric_difference;
}
my $duration = time - $start;
say "Duration: $duration seconds.";
However, on my small laptop (only 2 GByte RAM and running a lot of other programs and services) I get an "Out of memory" error, so two lists of 5 million proteins is too big for it. YMMV if you have a more performant machine. It runs fine and fast for 500,000 proteins (15 seconds), 1,000,000 proteins (52 seconds) and 2,000,000 proteins (185 seconds).
CountZero A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James
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[d/l] |
I'm not 100% sure what you want to do here Jeri. The sample below assumes you have a single string composed of 9 character sequences. When the 'for' has run the keys of %uniq will be the unique 9 character sequences.
It would take a while and a lot of memory over 5 mill x 9 char sequences!
my $str = join '',(648040620,637132715,649986572,648040620 );
my $proteins_count = length ($str)/9;
my %uniq;
do { $uniq{$_}++ unless $uniq{$_} }
for unpack "(A9)$proteins_count" , $str;
print "@{[keys %uniq]}\n";
Prints ..
637132715 648040620 649986572
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[d/l] |
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