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)'
Related
I'm using Perl to feed data to an LCD display. The display is 8 characters wide. The strings of data to be displayed are always significantly longer than 8 characters. As such, I need to break the strings down into "frames" of 8 characters or less, and feed the "frames" to the display one at a time.
The display is not intelligent enough to do this on its own. The only convenience it offers is that strings of less than 8 characters are automatically centered on the display.
In the beginning, I simply sent the string 8 characters at a time - here goes 1-8, now 9-16, now 17-24, etc. But that wasn't especially nice-looking. I'd like to do something better, but I'm not sure how best to approach it.
These are the constraints I'd like to implement:
Fit as many words into a "frame" as possible
No starting/trailing space(s) in a "frame"
Symbol (ie. hyphen, ampersand, etc) with a space on both sides qualifies as a word
If a word is longer than 8 characters, simulate per-character scrolling
Break words longer than 8 characters at a slash or hyphen
Some hypothetical input strings, and desired output for each...
Electric Light Orchestra - Sweet Talkin' Woman
Electric
Light
Orchestr
rchestra
- Sweet
Talkin'
Woman
Quarterflash - Harden My Heart
Quarterf
uarterfl
arterfla
rterflas
terflash
- Harden
My Heart
Steve Miller Band - Fly Like An Eagle
Steve
Miller
Band -
Fly Like
An Eagle
Hall & Oates - Did It In A Minute
Hall &
Oates -
Did It
In A
Minute
Bachman-Turner Overdrive - You Ain't Seen Nothing Yet
Bachman-
Turner
Overdriv
verdrive
- You
Ain't
Seen
Nothing
Yet
Being a relative Perl newbie, I'm trying to picture how would be best to handle this. Certainly I could split the string into an array of individual words. From there, perhaps I could loop through the array, counting the letters in each subsequent word to build the 8-character "frames". Upon encountering a word longer than 8 characters, I could then repetitively call substr on that word (with offset +1 each time), creating the illusion of scrolling.
Is this a reasonable way to accomplish my goal? Or am I reinventing the wheel here? How would you do it?
The base question is to find all consecutive overlapping N-long substrings in a compact way.
Here it is in one pass with a regex, and see the end for doing it using substr.
my $str = join '', "a".."k"; # 'Quarterflash';
my #eights = $str =~ /(?=(.{8}))/g;
This uses a lookahead which also captures, and in this way the regex crawls up the string character by character, capturing the "next" eight each time.
Once we are at it, here is also a basic solution for the problem. Add words to a buffer until it would exceed 8 characters, at which point it is added to an array of display-ready strings and cleared.
use warnings;
use strict;
use feature 'say';
my $str = shift // "Quarterflash - Harden My Heart";
my #words = split ' ', $str;
my #to_display;
my $buf = '';
foreach my $w (#words) {
if (length $w > 8) {
# Now have to process the buffer first then deal with this long word
push #to_display, $buf;
$buf = '';
push #to_display, $w =~ /(?=(.{8}))/g;
}
elsif ( length($buf) + 1 + length($w) > 8 ) {
push #to_display, $buf;
$buf = $w;
}
elsif (length $buf != 0) { $buf .= ' ' . $w }
else { $buf = $w }
}
push #to_display, $buf if $buf;
say for #to_display;
This is clearly missing some special/edge cases, in particular those involving non-word characters and hyphenated words, but that shouldn't be too difficult to add.†
Here is a way to get all consecutive 8-long substrings using substr
my #to_display = map { substr $str, $_, 8 } 0..length($str)-8;
† Example, break a word with hyphen/slash when it has no spaces around it (per question)
my #parts = split m{\s+|(?<=\S)[-/](?=\S)}, $w;
The hyphen/slash is discarded as this stands; that can be changed by capturing the pattern as well and then filtering out elements with only spaces
my #parts = grep { /\S/ } split m{( \s+ | (?<=\S) [-/] (?=\S) )}x, $w;
These haven't been tested beyond just barely. Can fit in the if (length $w > 8) branch.
The initial take-- The regex was originally written with a two-part pattern. Keeping it here for record and as an example of use of pair-handling functions from List::Util
The regex below matches and captures a character, followed by a lookahead for the next seven, which it also captures. This way the engine captures 1 and 7-long substrings as it moves along char by char. Then the consecutive pairs from the returned list are joined
my $str = join '', "a".."k"; # 'Quarterflash';
use List::Util qw(pairmap);
my #eights = pairmap { $a . $b } $str =~ /(. (?=(.{7})) )/gx;
# or
# use List::Util qw(pairs);
# my #eights = map { join '', #$_ } pairs $str =~ /(.(?=(.{7})))/g;
UPDATE
As pointed out in the answer, this question really has to do with Scalar versus List Context in Perl.
## ## ##
I am learning perl via self-taught crash course (primarily with the Llama book and the web). In attempting some byte swap code, I have found a one liner I do not understand completely. A comment in the script explains what I think is happening in the one-liner.
#!/usr/bin/perl --
#
# Script to print byte-swapped hex values
#
use 5.010;
use warnings;
use strict;
# NOTE: I realize I could use a single variable 'data', but the x- y- z- prefixes may help in
# identification (for clarity) in the code for this SO question.
my $xData;
my $yData;
my $zData;
for ( my $ijk = 998; $ijk < 1001; $ijk++ )
{
printf ( "\n%4d is hex " . (sprintf "0x%04X", $ijk) . "\n", $ijk );
# with byte swap
say "These numbers (bytes swapped) should match...";
# do sprintf, match pattern and store to ($1)($2), now reverse them into ($2)($1).
# BindOp leaves $_ alone, match stuffs $_ & is then used as input for reverse, prints.
say reverse ((sprintf "%04X", $ijk) =~ /(..)(..)/) ; # from perlmonks' webpage
$yData = (reverse ((sprintf "%04X", $ijk) =~ /(..)(..)/) );
say $yData; # does NOT match
$xData = sprintf "%04X", $ijk;
$xData =~ s/(..)(..)/$2$1/ ;
say $xData; # does match
$_ = sprintf "%04X", $ijk;
/(..)(..)/;
$zData = $2 . $1 ;
say $zData; # does match
}
exit 0;
OUTPUT:
998 is hex 0x03E6 These numbers (bytes swapped) should match...
E603
6E30
E603
E603
999 is hex 0x03E7 These numbers (bytes swapped) should match...
E703
7E30
E703
E703
1000 is hex 0x03E8 These numbers (bytes swapped) should match...
E803
8E30
E803
E803
Why does the one liner work, and why doesn't the $yData perform the same way? I'm pretty sure I understand why $xData and $zData work, but I would expect $yData to be the closest equivalent non-one-liner. What is the closest equivalent non-one-liner and why? Where is the discrepancy?
The reverse in your print (say) statement comes in the list context, while when assigned to $yData the context is scalar. This function (may) behave considerably differently based on the context.
From perldoc -f reverse
reverse LIST
In list context, returns a list value consisting of the elements of LIST in the opposite order. In scalar context, concatenates the elements of LIST and returns a string value with all characters in the opposite order.
In this case this produces different results.
When called in list context, it swaps the (two) input bytes, keeping each byte intact (represented by two hexadecimal digits matched in a group). When called in scalar context, it joins the input and returns a character string, running in the opposite order. Taken to represent a hex number this would have each byte changed.
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
I'm a student in an intro Perl class, looking for suggestions and feedback on my approach to writing a small (but tricky) program that analyzes data about atoms. My professor encourages forums. I am not advanced with Perl subs or modules (including Bioperl) so please limit responses to an appropriate 'beginner level' so that I can understand and learn from your suggestions and/or code (also limit "Magic" please).
The requirements of the program are as follows:
Read a file (containing data about Atoms) from the command line & create an array of atom records (one record/atom per newline). For each record the program will need to store:
• The atom's serial number (cols 7 - 11)
• The three-letter name of the amino acid to which it belongs (cols 18 - 20)
• The atom's three coordinates (x,y,z) (cols 31 - 54 )
• The atom's one- or two-letter element name (e.g. C, O, N, Na) (cols 77-78 )
Prompt for one of three commands: freq, length, density d (d is some number):
• freq - how many of each type of atom is in the file (example Nitrogen, Sodium, etc would be displayed like this: N: 918 S: 23
• length - The distances among coordinates
• density d (where d is a number) - program will prompt for the name of a file to save computations to and will containing the distance between that atom and every other atom. If that distance is less than or equal to the number d, it increments the count of the number of atoms that are within that distance, unless that count is zero into the file. The output will look something like:
1: 5
2: 3
3: 6
... (very big file) and will close when it finishes.
I'm looking for feedback on what I have written (and need to write) in the code below. I especially appreciate any feedback in how to approach writing my subs. I've included sample input data at the bottom.
The program structure and function descriptions as I see it:
$^W = 1; # turn on warnings
use strict; # behave!
my #fields;
my #recs;
while ( <DATA> ) {
chomp;
#fields = split(/\s+/);
push #recs, makeRecord(#fields);
}
for (my $i = 0; $i < #recs; $i++) {
printRec( $recs[$i] );
}
my %command_table = (
freq => \&freq,
length => \&length,
density => \&density,
help => \&help,
quit => \&quit
);
print "Enter a command: ";
while ( <STDIN> ) {
chomp;
my #line = split( /\s+/);
my $command = shift #line;
if ($command !~ /^freq$|^density$|length|^help$|^quit$/ ) {
print "Command must be: freq, length, density or quit\n";
}
else {
$command_table{$command}->();
}
print "Enter a command: ";
}
sub makeRecord
# Read the entire line and make records from the lines that contain the
# word ATOM or HETATM in the first column. Not sure how to do this:
{
my %record =
(
serialnumber => shift,
aminoacid => shift,
coordinates => shift,
element => [ #_ ]
);
return\%record;
}
sub freq
# take an array of atom records, return a hash whose keys are
# distinct atom names and whose values are the frequences of
# these atoms in the array.
sub length
# take an array of atom records and return the max distance
# between all pairs of atoms in that array. My instructor
# advised this would be constructed as a for loop inside a for loop.
sub density
# take an array of atom records and a number d and will return a
# hash whose keys are atom serial numbers and whose values are
# the number of atoms within that distance from the atom with that
# serial number.
sub help
{
print "To use this program, type either\n",
"freq\n",
"length\n",
"density followed by a number, d,\n",
"help\n",
"quit\n";
}
sub quit
{
exit 0;
}
# truncating for testing purposes. Actual data is aprox. 100 columns
# and starts with ATOM or HETATM.
__DATA__
ATOM 4743 CG GLN A 704 19.896 32.017 54.717 1.00 66.44 C
ATOM 4744 CD GLN A 704 19.589 30.757 55.525 1.00 73.28 C
ATOM 4745 OE1 GLN A 704 18.801 29.892 55.098 1.00 75.91 O
It looks like your Perl skills are advancing nicely -- using references and complex data structures. Here are a few tips and pieces of general advice.
Enable warnings with use warnings rather than $^W = 1. The former is self-documenting and has the advantage being local to the enclosing block rather than being a global setting.
Use well-named variables, which will help document the program's behavior, rather than relying on Perl's special $_. For example:
while (my $input_record = <DATA>){
}
In user-input scenarios, an endless loop provides a way to avoid repeated instructions like "Enter a command". See below.
Your regex can be simplified to avoid the need for repeated anchors. See below.
As a general rule, affirmative tests are easier to understand than negative tests. See the modified if-else structure below.
Enclose each part of program within its own subroutine. This is a good general practice for a bunch of reasons, so I would just start the habit.
A related good practice is to minimize the use of global variables. As an exercise, you could try to write the program so that it uses no global variables at all. Instead, any needed information would be passed around between the subroutines. With small programs one does not necessarily need to be rigid about the avoidance of globals, but it's not a bad idea to keep the ideal in mind.
Give your length subroutine a different name. That name is already used by the built-in length function.
Regarding your question about makeRecord, one approach is to ignore the filtering issue inside makeRecord. Instead, makeRecord could include an additional hash field, and the filtering logic would reside elsewhere. For example:
my $record = makeRecord(#fields);
push #recs, $record if $record->{type} =~ /^(ATOM|HETATM)$/;
An illustration of some of the points above:
use strict;
use warnings;
run();
sub run {
my $atom_data = load_atom_data();
print_records($atom_data);
interact_with_user($atom_data);
}
...
sub interact_with_user {
my $atom_data = shift;
my %command_table = (...);
while (1){
print "Enter a command: ";
chomp(my $reply = <STDIN>);
my ($command, #line) = split /\s+/, $reply;
if ( $command =~ /^(freq|density|length|help|quit)$/ ) {
# Run the command.
}
else {
# Print usage message for user.
}
}
}
...
FM's answer is pretty good. I'll just mention a couple of additional things:
You already have a hash with the valid commands (which is a good idea). There's no need to duplicate that list in a regex. I'd do something like this:
if (my $routine = $command_table{$command}) {
$routine->(#line);
} else {
print "Command must be: freq, length, density or quit\n";
}
Notice I'm also passing #line to the subroutine, because you'll need that for the density command. Subroutines that don't take arguments can just ignore them.
You could also generate the list of valid commands for the error message by using keys %command_table, but I'll leave that as an exercise for you.
Another thing is that the description of the input file mentions column numbers, which suggests that it's a fixed-width format. That's better parsed with substr or unpack. If a field is ever blank or contains a space, then your split will not parse it correctly. (If you use substr, be aware that it numbers columns starting at 0, when people often label the first column 1.)
I want to generate random hex values and those values should not be repetitive
and it should be of 4 bytes (ie: 0x00000000 to 0xffffffff) and the display output
should contain leading zeros.
For example: if I get the value 1 it should not represented as 0x1 but 0x00000001.
I want a minimum of 100 random values. Please tell me: how can I do that in Perl?
To get a random number in the range 0 .. (2<<32)-1:
my $rand = int(rand(0x100000000));
To print it in hex with leading zeroes:
printf "%08x", $rand;
Do please note this from the Perl man page:
Note: If your rand function consistently returns numbers that
are too large or too small, then your version of Perl was probably compiled with the wrong number of RANDBITS
If that's a concern, do this instead:
printf "%04x%04x", int(rand(0x10000)), int(rand(0x10000));
Note, also, that this does nothing to prevent repetition, although to be honest the chance of a repeating 32 bit number in a 100 number sequence is pretty small.
If it's absolutely essential that you don't repeat, do something like this:
my (%a); # create a hash table for remembering values
foreach (0 .. 99) {
my $r;
do {
$r = int(rand(0x100000000));
} until (!exists($a{$r})); # loop until the value is not found
printf "%08x\n", $r; # print the value
$a{$r}++; # remember that we saw it!
}
For what it's worth, this algorithm shouldn't be used if the range of possible values is less than (or even near to) the number of values required. That's because the random number generator loop will just repeatedly pull out numbers that were already seen.
However in this case where the possible range is so high (2^32) and the number of values wanted so low it'll work perfectly. Indeed with a range this high it's about the only practical algorithm.
perl -e 'printf "%08X\n", int rand 0xFFFFFFFF for 1 .. 100'
Alnitak explained it, but here's a much simpler implementation. I'm not sure how everyone starting reaching for do {} while since that's a really odd choice:
my $max = 0xFFFF_FFFF;
my( %Seen, #numbers );
foreach ( 1 .. 100 )
{
my $rand = int rand( $max + 1 );
redo if $Seen{$rand}++;
push #numbers, $rand;
}
print join "\n", map { sprintf "0x%08x", $_ } #numbers;
Also, as Alnitak pointed out, if you are generating a lot of numbers, that redo might cycle many, many times.
These will only be pseudorandom numbers, but you're not really asking for real random number anyway. That would involve possible repetition. :)
use LWP::Simple "get";
use List::MoreUtils "uniq";
print for uniq map { s/\t//, "0x$_" } split /^/, LWP::Simple::get('http://www.random.org/integers/?num=220&min=0&max=65535&col=2&base=16&format=plain&rnd=date.2009-12-14');
Adjust the url (see the form on http://www.random.org/integers/?mode=advanced) to not always return the same list. There is a minuscule chance of not returning at least 100 results.
Note that this answer is intentionally "poor" as a comment on the poor question. It's not a single question, it's a bunch all wrapped up together, all of which I'd bet have existing answers already (how do I generate a random number in range x, how do I format a number as a hex string with 0x and 0-padding, how do I add only unique values into a list, etc.). It's like asking "How do I write a webserver in Perl?" Without guessing what part the questioner really wants an answer to, you either have to write a tome for a response, or say something like:
perl -MIO::All -e 'io(":80")->fork->accept->(sub { $_[0] < io(-x $1 ? "./$1 |" : $1) if /^GET \/(.*) / })'
To get a random integer:
int(rand(0x10000000))
To format it as 8 hexadecimal digits:
printf "%08x", int(rand(0x10000000))