performance issue with substr on a very long UTF-8 string - perl

I am using substr on a very long UTF-8 string (~250,000,000 characters).
The thing is my program almost freeze around the 200,000,000th character.
Does somebody know about this issue? What are my options?
As I am indexing a document using a suffix array, I need:
to keep my string in one piece;
to access variable length substrings using an index.
As for a MWE:
use strict;
use warnings;
use utf8;
my $text = 'あいうえお' x 50000000;
for( my $i = 0 ; $i < length($text) ; $i++ ){
print "\r$i";
my $char = substr($text,$i,1);
}
print "\n";

Perl has two string storage formats. One that's capable of storing 8-bit characters, and one capable of storing 72-bit characters (practically limited to 32 or 64). Your string necessarily uses the latter format. This wide-character format uses a variable number of bytes per character like UTF-8 does.
Finding the ith element of a string in the first format is trivial: Add the offset to the string pointer. With the second format, finding the ith character requires scanning the string from the beginning, just like you would have to scan a file from the beginning to find the nth line. There is a mechanism that caches information about the string as it's discovered, but it's not perfect.
The problem goes away if you use a fixed number of bytes per character.
use utf8;
use Encode qw( encode );
my $text = 'あいうえお' x 50000000;
my $packed = encode('UCS-4le', $text);
for my $i (0..length($packed)/4) {
print "\r$i";
my $char = chr(unpack('V', substr($packed, $i*4, 4)));
}
print "\n";
Note that the string will use 33% more memory for hiragana characters. Or maybe not, since there's no cache anymore.

I suggest that you use a regular expression instead of substr.
Benchmarking these two methods shows that a regex is nearly 100 times faster:
use strict;
use warnings;
use utf8;
my $text = 'あいうえお' x 50_000;
sub mysubstr {
for( my $i = 0 ; $i < length($text) ; $i++ ){
my $char = substr($text,$i,1);
}
}
sub myregex {
while ($text =~ /(.)/g) {
my $char = $1;
}
}
use Benchmark qw(:all) ;
timethese(10, {
'substr' => \&mysubstr,
'regex' => \&myregex,
});
Outputs:
Benchmark: timing 10 iterations of regex, substr...
regex: 2 wallclock secs ( 2.18 usr + 0.00 sys = 2.18 CPU) # 4.58/s (n=10)
substr: 198 wallclock secs (184.66 usr + 0.16 sys = 184.81 CPU) # 0.05/s (n=10)

It is a known issue listed under Bugs for Perl 5.20.0:
http://perldoc.perl.org/perlunicode.html#Speed
The most important part is the first paragraph of my quote:
Speed
Some functions are slower when working on UTF-8 encoded strings than on byte encoded strings. All functions that need to hop over characters such as length(), substr() or index(), or matching regular expressions can work much faster when the underlying data are byte-encoded.
In Perl 5.8.0 the slowness was often quite spectacular; in Perl 5.8.1 a caching scheme was introduced which will hopefully make the slowness somewhat less spectacular, at least for some operations. In general, operations with UTF-8 encoded strings are still slower. As an example, the Unicode properties (character classes) like \p{Nd} are known to be quite a bit slower (5-20 times) than their simpler counterparts like \d (then again, there are hundreds of Unicode characters matching Nd compared with the 10 ASCII characters matching d ).
The easiest way to avoid it is using byte-strings instead of unicode-strings.

In your particular sample, you can just remove characters from the beginning of the $text string as they are processed in order to avoid the linear lookup:
use utf8;
use Encode qw( encode );
$| = 1;
my $text = 'あいうえお' x 50000000;
while ($text ne '') {
print ".";
my $char = substr($text, 0, 1, '');
}
print "\n";

Related

truncate string in perl into substring with trailing elipses

I'm trying to truncate a string in a select input option using perl if it is longer than a set value, though i can't get it to work correctly.
my $value = defined $option->{value} ? $option->{value} : '';
my $maxValueLength = 50;
if ($value.length > $maxValueLength) {
$value = substr $value, 0, $maxValueLength + '...';
}
Another option is regex
$string =~ s/.{$maxLength}\K.*/.../;
It matches any character (.) given number of times ({N}, here $maxLength), what is the first $maxLength characters in $string; then \K makes it "forget" all previous matches so those won't get replaced later. The rest of the string that is matched is then replaced by ...
See Lookaround assertions in perlre for \K.
This does start the regex engine for a simple task but it doesn't need any conditionals -- if the string is shorter than the maximum length the regex won't match and nothing happens.
Your code has several syntax errors. Turn on use strict and use warnings if you don't have it, and then read the error messages it tells you about. This is a bit tricky because of Perl's very complex syntax (see also Damian Conway's keynote from the 2020 Perl and Raku Conference), but it boils down to these:
Use of uninitialized value in concatenation (.) or string at line 7
Argument "..." isn't numeric in addition (+) at line 8
I've used the following adaption of your code to produce these
use strict;
use warnings;
my $value = '1234567890' x 10;
my $maxValueLength = 50;
if ( $value.length > $maxValueLength ) {
$value = substr $value, 0, $maxValueLength + '...';
}
print $value;
Now let's see what they mean.
The . operator in Perl is a concatenation. You cannot use it to call methods, and length is not a method on a string. Perl thinks you are using the built-in length (a function, not a method) without an argument, which makes it default to $_. Most built-ins do this, to make one-liners shorter. But $_ is not defined. Now the . tries to concatenate the length of undef to $value. And using undef in a string operation leads to this warning.
The correct way of doing this is length $value (or with parentheses if you prefer them, length($value)).
The + operator is not concatenation (we just learned that the . is). It's a numerical addition. Perl is pretty good at converting between strings and numbers as there aren't really any types, so saying 1 + "5" would give you 6 without problems, but it cannot do that for a couple of dots in a string. Hence it complains about a non-number value in an addition.
You want the substring with a given length, and then you want to attach the three dots. Because of associativity (or stickyness) of operators you will need to use parentheses () for your substr call.
$value = substr($value, 0, $maxValueLength) . '...';
To find a length of the string use length(STRING)
Here is the code snippet how you can modify the script.
#!/usr/bin/perl
use strict;
use warnings;
use feature qw(say);
my $string = "abcdefghijklmnopqrstuvwxyz abcdefghijklmnopqrstuvwxyz abcdefghijklmnopqrstuvwxyz";
say "length of original string is:".length($string);
my $value = defined $string ? $string : '';
my $maxValueLength = 50;
if (length($value) > $maxValueLength) {
$value = substr $value, 0, $maxValueLength;
say "value:$value";
say "value's length:".length($value);
}
Output:
length of original string is:80
value:abcdefghijklmnopqrstuvwxyz abcdefghijklmnopqrstuvw
value's length:50

Shortest Perl solution for outputing 4 random words

I have this one-line Unix shell script
for i in 1 2 3 4; do sed "$(tr -dc '0-9' < /dev/urandom | fold -w 5 |
awk '$0>=35&&$0<=65570' | head -1)q;d" "$0"; done | perl -p00e
's/\n(?!\Z)/ /g'
The script has 65K words in it, one per line, from line 35 to 65570. The code and the data are in the same file.
This script outputs 4 space-separated random words from this list with a newline at the end. For example
first fourth third second
How can I make this one-liner much shorter with Perl, keeping the
tr -dc '0-9' < /dev/urandom
part?
Keeping it is important since it provides Cryptographically Secure Pseudo-Random Numbers (CSPRNs) for all Unix OSs. Of course, if Perl can get numbers from /dev/urandom then the tr can be replaced with Perl too, but the numbers from urandom need to stay.
For convenience, I shared the base script with 65K words
65kwords.txt
or
65kwords.txt
Please use only core modules. It would be used for generating "human memorable passwords".
Later, the (hashing) iteration count, where we would use this to store the passwords would be extremely high, so brute-force would be very slow, even with many many GPUs/FPGAs.
You mention needing a CSPRN, which makes this a non trivial exercise - if you need cryptographic randomness, then using built in stuff (like rand) is not a good choice, as the implementation is highly variable across platforms.
But you've got Rand::Urandom which looks like it does the trick:
By default it uses the getentropy() (only available in > Linux 3.17) and falls back to /dev/arandom then /dev/urandom.
#!/usr/bin/env perl
use strict;
use warnings;
use Rand::Urandom;
chomp ( my #words = <DATA> );
print $words[rand #words], " " for 1..4;
print "\n";
__DATA__
yarn
yard
wound
worst
worry
work
word
wool
wolf
wish
wise
wipe
winter
wing
wind
wife
whole
wheat
water
watch
walk
wake
voice
Failing that though - you can just read bytes from /dev/urandom directly:
#!/usr/bin/env perl
use strict;
use warnings;
my #number_of_words = 4;
chomp ( my #words = <DATA> );
open ( my $urandom, '<:raw', '/dev/urandom' ) or die $!;
my $bytes;
read ( $urandom, $bytes, 2 * $number_of_words ); #2 bytes 0 - 65535
#for testing
#unpack 'n' is n An unsigned short (16-bit)
# unpack 'n*' in a list context returns a list of these.
foreach my $value ( unpack ( "n*", $bytes ) ) {
print $value,"\n";
}
#actually print the words.
#note - this assumes that you have the right number in your list.
# you could add a % #words to the map, e.g. $words[$_ % #words]
#but that will mean wrapping occurs, and will alter the frequency distribution.
#a more robust solution would be to fetch additional bytes if the 'slot' is
#empty.
print join " ", ( map { $words[$_] } unpack ( "n*", $bytes )),"\n";
__DATA__
yarn
yard
wound
worst
#etc.
Note - the above relies on the fact that your wordlist is the same size as two bytes (16 bits) - if this assumption isn't true, you'll need to deal with 'missed' words. A crude approach would be to take a modulo, but that would mean some wrapping and therefore not quite truly even distribution of word picks. Otherwise you can bit-mask and reroll, as indicated below:
On a related point though - have you considered not using a wordlist, and instead using consonant-vowel-consonant groupings?
E.g.:
#!/usr/bin/env perl
use strict;
use warnings;
#uses /dev/urandom to fetch bytes.
#generates consonant-vowel-consonant groupings.
#each are 11.22 bits of entropy, meaning a 4-group is 45 bits.
#( 20 * 6 * 20 = 2400, which is 11.22 bits of entropy log2 2400
#log2(2400 ^ 4) = 44.91
#but because it's generated 'true random' it's a know entropy string.
my $num = 4;
my $format = "CVC";
my %letters = (
V => [qw ( a e i o u y )],
C => [ grep { not /[aeiouy]/ } "a" .. "z" ], );
my %bitmask_for;
foreach my $type ( keys %letters ) {
#find the next power of 2 for the number of 'letters' in the set.
#So - for the '20' letter group, that's 31. (0x1F)
#And for the 6 letter group that's 7. (0x07)
$bitmask_for{$type} = ( 2 << log ( #{$letters{$type}} ) / log 2 ) - 1 ;
}
open( my $urandom, '<:raw', '/dev/urandom' ) or die $!;
for ( 1 .. $num ) {
for my $type ( split //, $format ) {
my $value;
while ( not defined $value or $value >= #{ $letters{$type} } ) {
my $byte;
read( $urandom, $byte, 1 );
#byte is 0-255. Our key space is 20 or 6.
#So rather than modulo, which would lead to an uneven distribution,
#we just bitmask and discard and 'too high'.
$value = (unpack "C", $byte ) & $bitmask_for{$type};
}
print $letters{$type}[$value];
}
print " ";
}
print "\n";
close($urandom);
This generates 3 character CVC symbols, with a known entropy level (11.22 per 'group') for making reasonably robust passwords. (45 bits as opposed to the 64 bits of your original, although obviously you can add extra 'groups' to gain 11.22 bits per time).
This answer is not cryptographically safe!
I would do this completely in Perl. No need for a one-liner. Just grab your word-list and put it into a Perl program.
use strict;
use warnings;
my #words = qw(
first
second
third
fourth
);
print join( q{ }, map { $words[int rand #words] } 1 .. 4 ), "\n";
This grabs four random words from the list and outputs them.
rand #words evaluates #words in scalar context, which gives the number of elements, and creates a random floating point value between 0 and smaller than that number. int cuts off the decimals. This is used as the index to grab an element out of #words. We repeat this four times with the map statement, where the 1 .. 4 is the same as passing a list of (1, 2, 3, 4) into map as an argument. This argument is ignored, but instead our random word is picked. map returns a list, which we join on one space. Finally we print the resulting string, and a newline.
The word list is created with the quoted words qw() operator, which returns a list of quoted words. It's shorthand so you don't need to type all the quotes ' and commas ,.
If you'd want to have the word list at the bottom you could either put the qw() in a sub and call it at the top, or use a __DATA__ section and read from it like a filehandle.
The particular method using tr and fold on /dev/urandom is a lot less efficient than it could be, so let's fix it up a little bit, while keeping the /dev/urandom part.
Assuming that available memory is enough to contain your script (including wordlist):
chomp(#words = <DATA>);
open urandom, "/dev/urandom" or die;
read urandom, $randbytes, 4 * 2 or die;
print join(" ", map $words[$_], unpack "S*", $randbytes), "\n";
__DATA__
word
list
goes
here
This goes for brevity and simplicity without outright obfuscation — of course you could make it shorter by removing whitespace and such, but there's no reason to. It's self-contained and will work with several decades of perls (yes, those bareword filehandles are deliberate :-P)
It still expects exactly 65536 entries in the wordlist, because that way we don't have to worry about introducing bias to the random number choice using a modulus operator. A slightly more ambitious approach might be to read 48 bytes from urandom for each word, turning it into a floating-point value between 0 and 1 (portable to most systems) and multiplying it by the size of the word list, allowing for a word list of any reasonable size.
A lot of nonsense is talked about password strength, and I think you're overestimating the worth of several of your requirements here
I don't understand your preoccupation with making your code "much shorter with perl". (Why did you pick Perl?) Savings here can only really be useful to make the script quicker to read and compile, but they will be dwarfed by the half megabyte of data following the code which must also be read
In this context, the usefulness to a hacker of a poor random number generator depends on prior knowledge of the construction of the password together with the passwords that have been most recently generated. With a sample of only 65,000 words, even the worst random number generator will show insignificant correlation between successive passwords
In general, a password is more secure if it is longer, regardless of its contents. Forming a long password out of a sequence of English words is purely a way of making the sequence more memorable
"Of course later, the (hashing) iteration count ... would be extreme high, so brute-force [hacking?] would be very slow"
This doesn't follow at all. Cracking algorithms won't try to guess the four words you've chosen: they will see only a thirty-character (or so) string consisting only of lower-case letters and spaces, and whose origin is insignificant. It will be no more or less crackable than any other password of the same length with the same character set
I suggest that you should rethink your requirements and so make things easier for yourself. I don't find it hard to think of four English words, and don't need a program to do it for me. Hint: pilchard is a good one: they never guess that!
If you still insist, then I would write something like this in Perl. I've used only the first 18 lines of your data for
use strict;
use warnings 'all';
use List::Util 'shuffle';
my #s = map /\S+/g, ( shuffle( <DATA> ) )[ 0 .. 3 ];
print "#s\n";
__DATA__
yarn
yard
wound
worst
worry
work
word
wool
wolf
wish
wise
wipe
winter
wing
wind
wife
whole
wheat
output
wind wise winter yarn
You could use Data::Random::rand_words()
perl -MData::Random -E 'say join $/, Data::Random::rand_words(size => 4)'

Count subsequences in hundreds of GB of data

I'm trying to process a very large file and tally the frequency of all sequences of a certain length in the file.
To illustrate what I'm doing, consider a small input file containing the sequence abcdefabcgbacbdebdbbcaebfebfebfeb
Below, the code reads the whole file in, and takes the first substring of length n (below I set this to 5, although I want to be able to change this) and counts its frequency:
abcde => 1
Next line, it moves one character to the right and does the same:
bcdef => 1
It then continues for the rest of the string and prints the 5 most frequent sequences:
open my $in, '<', 'in.txt' or die $!; # 'abcdefabcgbacbdebdbbcaebfebfebfeb'
my $seq = <$in>; # read whole file into string
my $len = length($seq);
my $seq_length = 5; # set k-mer length
my %data;
for (my $i = 0; $i <= $len - $seq_length; $i++) {
my $kmer = substr($seq, $i, $seq_length);
$data{$kmer}++;
}
# print the hash, showing only the 5 most frequent k-mers
my $count = 0;
foreach my $kmer (sort { $data{$b} <=> $data{$a} } keys %data ){
print "$kmer $data{$kmer}\n";
$count++;
last if $count >= 5;
}
ebfeb 3
febfe 2
bfebf 2
bcaeb 1
abcgb 1
However, I would like to find a more efficient way of achieving this. If the input file was 10GB or 1000GB, then reading the whole thing into a string would be very memory expensive.
I thought about reading in blocks of characters, say 100 at a time and proceeding as above, but here, sequences that span 2 blocks would not be tallied correctly.
My idea then, is to only read in n number of characters from the string, and then move onto the next n number of characters and do the same, tallying their frequency in a hash as above.
Are there any suggestions about how I could do this? I've had a look a read using an offset, but can't get my head around how I could incorporate this here
Is substr the most memory efficient tool for this task?
From your own code it's looking like your data file has just a single line of data -- not broken up by newline characters -- so I've assumed that in my solution below. Even if it's possible that the line has one newline character at the end, the selection of the five most frequent subsequences at the end will throw this out as it happens only once
This program uses sysread to fetch an arbitrarily-sized chunk of data from the file and append it to the data we already have in memory
The body of the loop is mostly similar to your own code, but I have used the list version of for instead of the C-style one as it is much clearer
After processing each chunk, the in-memory data is truncated to the last SEQ_LENGTH-1 bytes before the next cycle of the loop pulls in more data from the file
I've also use constants for the K-mer size and the chunk size. They are constant after all!
The output data was produced with CHUNK_SIZE set to 7 so that there would be many instances of cross-boundary subsequences. It matches your own required output except for the last two entries with a count of 1. That is because of the inherent random order of Perl's hash keys, and if you require a specific order of sequences with equal counts then you must specify it so that I can change the sort
use strict;
use warnings 'all';
use constant SEQ_LENGTH => 5; # K-mer length
use constant CHUNK_SIZE => 1024 * 1024; # Chunk size - say 1MB
my $in_file = shift // 'in.txt';
open my $in_fh, '<', $in_file or die qq{Unable to open "$in_file" for input: $!};
my %data;
my $chunk;
my $length = 0;
while ( my $size = sysread $in_fh, $chunk, CHUNK_SIZE, $length ) {
$length += $size;
for my $offset ( 0 .. $length - SEQ_LENGTH ) {
my $kmer = substr $chunk, $offset, SEQ_LENGTH;
++$data{$kmer};
}
$chunk = substr $chunk, -(SEQ_LENGTH-1);
$length = length $chunk;
}
my #kmers = sort { $data{$b} <=> $data{$a} } keys %data;
print "$_ $data{$_}\n" for #kmers[0..4];
output
ebfeb 3
febfe 2
bfebf 2
gbacb 1
acbde 1
Note the line: $chunk = substr $chunk, -(SEQ_LENGTH-1); which sets $chunk as we pass through the while loop. This ensures that strings spanning 2 chunks get counted correctly.
The $chunk = substr $chunk, -4 statement removes all but the last four characters from the current chunk so that the next read appends CHUNK_SIZE bytes from the file to those remaining characters. This way the search will continue, but starts with the last 4 of the previous chunk's characters in addition to the next chunk: data doesn't fall into a "crack" between the chunks.
Even if you don't read the entire file into memory before processing it, you could still run out of memory.
A 10 GiB file contains almost 11E9 sequences.
If your sequences are sequences of 5 characters chosen from a set of 5 characters, there are only 55 = 3,125 unique sequences, and this would easily fit in memory.
If your sequences are sequences of 20 characters chosen from a set of 5 characters, there are 520 = 95E12 unique sequences, so the all 11E9 sequences of a 10 GiB file could unique. That does not fit in memory.
In that case, I suggest doing the following:
Create a file that contains all the sequences of the original file.
The following reads the file in chunks rather than all at once. The tricky part is handling sequences that span two blocks. The following program uses sysread[1] to fetch an arbitrarily-sized chunk of data from the file and append it to the last few character of the previously read block. This last detail allows sequences that span blocks to be counted.
perl -e'
use strict;
use warnings qw( all );
use constant SEQ_LENGTH => 20;
use constant CHUNK_SIZE => 1024 * 1024;
my $buf = "";
while (1) {
my $size = sysread(\*STDIN, $buf, CHUNK_SIZE, length($buf));
die($!) if !defined($size);
last if !$size;
for my $offset ( 0 .. length($buf) - SEQ_LENGTH ) {
print(substr($buf, $offset, SEQ_LENGTH), "\n");
}
substr($buf, 0, -(SEQ_LENGTH-1), "");
}
' <in.txt >sequences.txt
Sort the sequences.
sort sequences.txt >sorted_sequences.txt
Count the number of instances of each sequeunces, and store the count along with the sequences in another file.
perl -e'
use strict;
use warnings qw( all );
my $last = "";
my $count;
while (<>) {
chomp;
if ($_ eq $last) {
++$count;
} else {
print("$count $last\n") if $count;
$last = $_;
$count = 1;
}
}
' sorted_sequences.txt >counted_sequences.txt
Sort the sequences by count.
sort -rns counted_sequences.txt >sorted_counted_sequences.txt
Extract the results.
perl -e'
use strict;
use warnings qw( all );
my $last_count;
while (<>) {
my ($count, $seq) = split;
last if $. > 5 && $count != $last_count;
print("$seq $count\n");
$last_count = $count;
}
' sorted_counted_sequences.txt
This also prints ties for 5th place.
This can be optimized by tweaking the parameters passed to sort[2], but it should offer decent performance.
sysread is faster than previously suggested read since the latter performs a series of 4 KiB or 8 KiB reads (depending on your version of Perl) internally.
Given the fixed-length nature of the sequence, you could also compress the sequences into ceil(log256(520)) = 6 bytes then base64-encode them into ceil(6 * 4/3) = 8 bytes. That means 12 fewer bytes would be needed per sequence, greatly reducing the amount to read and to write.
Portions of this answer was adapted from content by user:622310 licensed under cc by-sa 3.0.
Generally speaking Perl is really slow at character-by-character processing solutions like those posted above, it's much faster at something like regular expressions since essentially your overhead is mainly how many operators you're executing.
So if you can turn this into a regex-based solution that's much better.
Here's an attempt to do that:
$ perl -wE 'my $str = "abcdefabcgbacbdebdbbcaebfebfebfeb"; for my $pos (0..4) { $str =~ s/^.// if $pos; say for $str =~ m/(.{5})/g }'|sort|uniq -c|sort -nr|head -n 5
3 ebfeb
2 febfe
2 bfebf
1 gbacb
1 fabcg
I.e. we have our string in $str, and then we pass over it 5 times generating sequences of 5 characters, after the first pass we start chopping off a character from the front of the string. In a lot of languages this would be really slow since you'd have to re-allocate the entire string, but perl cheats for this special case and just sets the index of the string to 1+ what it was before.
I haven't benchmarked this but I bet something like this is a much more viable way to do this than the algorithms above, you could also do the uniq counting in perl of course by incrementing a hash (with the /e regex option is probably the fastest way), but I'm just offloading that to |sort|uniq -c in this implementation, which is probably faster.
A slightly altered implementation that does this all in perl:
$ perl -wE 'my $str = "abcdefabcgbacbdebdbbcaebfebfebfeb"; my %occur; for my $pos (0..4) { substr($str, 0, 1) = "" if $pos; $occur{$_}++ for $str =~ m/(.{5})/gs }; for my $k (sort { $occur{$b} <=> $occur{$a} } keys %occur) { say "$occur{$k} $k" }'
3 ebfeb
2 bfebf
2 febfe
1 caebf
1 cgbac
1 bdbbc
1 acbde
1 efabc
1 aebfe
1 ebdbb
1 fabcg
1 bacbd
1 bcdef
1 cbdeb
1 defab
1 debdb
1 gbacb
1 bdebd
1 cdefa
1 bbcae
1 bcgba
1 bcaeb
1 abcgb
1 abcde
1 dbbca
Pretty formatting for the code behind that:
my $str = "abcdefabcgbacbdebdbbcaebfebfebfeb";
my %occur;
for my $pos (0..4) {
substr($str, 0, 1) = "" if $pos;
$occur{$_}++ for $str =~ m/(.{5})/gs;
}
for my $k (sort { $occur{$b} <=> $occur{$a} } keys %occur) {
say "$occur{$k} $k";
}
The most straightforward approach is to use the substr() function:
% time perl -e '$/ = \1048576;
while ($s = <>) { for $i (0..length $s) {
$hash{ substr($s, $i, 5) }++ } }
foreach my $k (sort { $hash{$b} <=> $hash{$a} } keys %hash) {
print "$k $hash{$k}\n"; $it++; last if $it == 5;}' nucleotide.data
NNCTA 337530
GNGGA 337362
NCACT 337304
GANGN 337290
ACGGC 337210
269.79 real 268.92 user 0.66 sys
The Perl Monks node on iterating along a string was a useful resource, as were the responses and comments from #Jonathan Leffler, #ÆvarArnfjörðBjarmason, #Vorsprung, #ThisSuitIsBlackNotm #borodin and #ikegami here in this SO posting. As was pointed out, the issue with very large files is memory, which in turn requires that files be read in chunks. When reading from a file in chunks, if your code is iterating through the data it has to properly handle switching from one chunk/source to the next without dropping any bytes.
As a simplistic example, next unless length $kmer == 5; will get checked during each 1048576 byte/character iteration in the script above, meaning strings that exist at the end of one chunk and the beginning of another will be missed (cf. #ikegami's and #Borodin's solutions). This will alter the resulting count, though perhaps not in a statistically significant way[1]. Both #borodin and #ikegami address the issue of missing/overlapping strings between chunks by appending each chunk to the remaining characters of the previous chunk as they sysread in their while() loops. See Borodin's response and comments for an explanation of how it works.
Using Stream::Reader
Since perl has been around for quite a while and has collected a lot of useful code, another perfectly valid approach is to look for a CPAN module that achieves the same end. Stream::Reader can create a "stream" interface to a file handle that wraps the solution to the chunking issue behind a set of convenient functions for accessing the data.
use Stream::Reader;
use strict;
use warnings;
open( my $handler, "<", shift );
my $stream = Stream::Reader->new( $handler, { Mode => "UB" } );
my %hash;
my $string;
while ($stream->readto("\n", { Out => \$string }) ) {
foreach my $i (0..length $string) {
$hash{ substr($string, $i, 5) }++
}
}
my $it;
foreach my $k (sort { $hash{$b} <=> $hash{$a} } keys %hash ) {
print "$k $hash{$k}\n";
$it++; last if $it == 5;
}
On a test data file nucleotide.data, both Borodin's script and the Stream::Reader approach shown above produced the same top five results. Note the small difference compared to the results from the shell command above. This illustrates the need to properly handle reading data in chunks.
NNCTA 337530
GNGGA 337362
NCACT 337305
GANGN 337290
ACGGC 337210
The Stream::Reader based script was significantly faster:
time perl sequence_search_stream-reader.pl nucleotide.data
252.12s
time perl sequence_search_borodin.pl nucleotide.data
350.57s
The file nucleotide.data was a 1Gb in size, consisting of single string of approximately 1 billion characters:
% wc nucleotide.data
0 0 1048576000 nucleotide.data
% echo `head -c 20 nucleotide.data`
NCCANGCTNGGNCGNNANNA
I used this command to create the file:
perl -MString::Random=random_regex -e '
open (my $fh, ">>", "nucleotide.data");
for (0..999) { print $fh random_regex(q|[GCNTA]{1048576}|) ;}'
Lists and Strings
Since the application is supposed to read a chunk at a time and move this $seq_length sized window along the length of the data building a hash for tracking string frequency, I thought a "lazy list" approach might work here. But, to move a window through a collection of data (or slide as with List::Gen) reading elements natatime, one needs a list.
I was seeing the data as one very long string which would first have to be made into a list for this approach to work. I'm not sure how efficient this can be made. Nevertheless, here is my attempt at a "lazy list" approach to the question:
use List::Gen 'slide';
$/ = \1048575; # Read a million character/bytes at a time.
my %hash;
while (my $seq = <>) {
chomp $seq;
foreach my $kmer (slide { join("", #_) } 5 => split //, $seq) {
next unless length $kmer == 5;
$hash{$kmer}++;
}
}
foreach my $k (sort { $hash{$b} <=> $hash{$a} } keys %hash) {
print "$k $hash{$k}\n";
$it++; last if $it == 5;
}
I'm not sure this is "typical perl" (TIMTOWDI of course) and I suppose there are other techniques (cf. gather/take) and utilities suitable for this task. I like the response from #Borodin best since it seems to be the most common way to take on this task and is more efficient for the potentially large file sizes that were mentioned (100Gb).
Is there a fast/best way to turn a string into a list or object? Using an incremental read() or sysread() with substr wins on this point, but even with sysread a 1000Gb string would require a lot of memory just for the resulting hash. Perhaps a technique that serialized/cached the hash to disk as it grew beyond a certain size would work with very, very large strings that were liable to create very large hashes.
Postscript and Results
The List::Gen approach was consistently between 5 and 6 times slower than #Borodin's approach. The fastest script used the Stream::Reader module. Results were consistent and each script selected the same top five strings with the two smaller files:
1 million character nucleotide string
sequence_search_stream-reader.pl : 0.26s
sequence_search_borodin.pl : 0.39s
sequence_search_listgen.pl : 2.04s
83 million character nucleotide string
With the data in file xaa:
wc xaa
0 1 83886080 xaa
% time perl sequence_search_stream-reader.pl xaa
GGCNG 31510
TAGNN 31182
AACTA 30944
GTCAN 30792
ANTAT 30756
21.33 real 20.95 user 0.35 sys
% time perl sequence_search_borodin.pl xaa
GGCNG 31510
TAGNN 31182
AACTA 30944
GTCAN 30792
ANTAT 30756
28.13 real 28.08 user 0.03 sys
% time perl sequence_search_listgen.pl xaa
GGCNG 31510
TAGNN 31182
AACTA 30944
GTCAN 30792
ANTAT 30756
157.54 real 156.93 user 0.45 sys
1 billion character nucleotide string
In a larger file the differences were of similar magnitude but, because as written it does not correctly handle sequences spanning chunk boundaries, the List::Gen script had the same discrepancy as the shell command line at the beginning of this post. The larger file meant a number of chunk boundaries and a discrepancy in the count.
sequence_search_stream-reader.pl : 252.12s
sequence_search_borodin.pl : 350.57s
sequence_search_listgen.pl : 1928.34s
The chunk boundary issue can of course be resolved, but I'd be interested to know about other potential errors or bottlenecks that are introduced using a "lazy list" approach. If there were any benefit in terms of CPU usage from using slide to "lazily" move along the string, it seems to be rendered moot by the need to make a list out of the string before starting.
I'm not surprised that reading data across chunk boundaries is left as an implementation exercise (perhaps it cannot be handled "magically") but I wonder what other CPAN modules or well worn subroutine style solutions might exist.
1. Skipping four characters - and thus four 5 character string combinations - at the end of each megabyte read of a terabyte file would mean the results would not include 3/10000 of 1% from the final count.
echo "scale=10; 100 * (1024^4/1024^2 ) * 4 / 1024^4 " | bc
.0003814697

Replace binary form 0->1 and 1->0 value - perl

In my script i am dealing with binary value and i need to replace 0->1 and 1->0 at one place.
example :
input digit = 10101001
output digit = 01010110
I tried $string =~ s/1/0/; and reverse function but that is getting fail to give me correct out put.
can some one help me out.
Use tr:
my $str = '10101001';
$s =~ tr/01/10/;
print "$s\n";
Outputs:
01010110
If your input string has only those two possibilities 0 and 1, then you can use substitution in a multi-stage approach:
$str =~ s/1/x/g; # all 1's to x
$str =~ s/0/1/g; # all 0's to 1
$str =~ s/x/0/g; # all x's to 0
This is not a bad option for languages that only provide substitutions, but Perl also has an atomic translation feature:
$str =~ tr/01/10/;
which will work just as well (better, really, since it's less code and probably less passes over the data).
You could also go mathy on this and use the bitwise XOR operator ^...
my $input = '10101001';
my $binval = oct( '0b'.$input );
my $result = $binval ^ 0b11111111;
printf "%08b\n", $result;
...which will also give you 01010110.
This of course has the downside of being dependent on the length of the bit input string. The given solution only works for 8-bit values. It wouldn't be hard to generalize for any number of bits, though.
To incorporate Lưu Vĩnh Phúc's comment - you can also use the bitwise NOT operator ~. Again, the implementation is dependent on the number of bits as you need to truncate the result:
my $input = '10101001';
my $binval = oct( '0b'.$input );
print substr( sprintf ( '%b', ~$binval ), -8 )."\n";

perl-how to treat a string as a binary number?

Read a file that contains an address and a data, like below:
#0, 12345678
#1, 5a5a5a5a
...
My aim is to read the address and the data. Consider the data I read is in hex format, and then I need to unpack them to binary number.
So 12345678 would become 00010010001101000101011001111000
Then, I need to further unpack the transferred binary number to another level.
So it becomes, 00000000000000010000000000010000000000000001000100000001000000000000000100000001000000010001000000000001000100010001000000000000
They way I did is like below
while(<STDIN>) {
if (/\#(\S+)\s+(\S+)/) {
$addr = $1;
$data = $2;
$mem{$addr} = ${data};
}
}
foreach $key (sort {$a <=> $b} (keys %mem)) {
my $str = unpack ('B*', pack ('H*',$mem{$key}));
my $str2 = unpack ('B*', pack ('H*', $str));
printf ("#%x ", $key);
printf ("%s",$str2);
printf ("\n");
}
It works, however, my next step is to do some numeric operation on the transferred bits.
Such as bitwise or and shifting. I tried << and | operator, both are for numbers, not strings. So I don't know how to solve this.
Please leave your comments if you have better ideas. Thanks.
You can employ Bit::Vector module from metaCPAN
use strict;
use warnings;
use Bit::Vector;
my $str = "1111000011011001010101000111001100010000001111001010101000111010001011";
printf "orig str: %72s\n", $str;
#only 72 bits for better view
my $vec = Bit::Vector->new_Bin(72,$str);
printf "vec : %72s\n", $vec->to_Bin();
$vec->Move_Left(2);
printf "left 2 : %72s\n", $vec->to_Bin();
$vec->Move_Right(4);
printf "right 4 : %72s\n", $vec->to_Bin();
prints:
orig str: 1111000011011001010101000111001100010000001111001010101000111010001011
vec : 001111000011011001010101000111001100010000001111001010101000111010001011
left 2 : 111100001101100101010100011100110001000000111100101010100011101000101100
right 4 : 000011110000110110010101010001110011000100000011110010101010001110100010
If you need do some math with arbitrary precision, you can also use Math::BigInt or use bigint (http://perldoc.perl.org/bigint.html)
Hex and binary are text representation of numbers. Shifting and bit manipulations are numerical operations. You want a number, not text.
my $hex = '5a5a5a5a';
$num = hex($hex); # Convert to number.
$num >>= 1; # Manipulate the number.
$hex = sprintf('%08X', $num); # Convert back to hex.
In a comment, you mention you want to deal with 256 bit numbers. The native numbers don't support that, but you can use Math::BigInt.
My final solution of this is forget about treat them as numbers, just treat them as string . I use substring and string concentration instead of shift. Then for the or operation , I just add each bit of the string, if it's 0 the result is 0, else is 1.
It may not be the best way to solve this problem. But that's the way I finally used.