Beefy Boxes and Bandwidth Generously Provided by pair Networks
Don't ask to ask, just ask

comment on

( #3333=superdoc: print w/replies, xml ) Need Help??

The task at hand shouts "RLE!!!" at me. General purpose RLE, efficiently (let's hope so) implemented (i.e. coded in C), accessed from Perl -- why, PDL, of course.

The benchmark below is probably very skewed because my test DNA consists of only short same base (nucleotide) fragments. Let's assume the ultimate goal is length of longest "C's" string and its position. The only other contestant is salva's code, modified to fit stated purpose. Sorry if I missed faster other monks' solution.

Note: sneaking Perl's scalar as PDL raw data looks hackish, which it is. Opening scalar as filehandle and then using readflex to stuff PDL raw data is, alas, too slow.

use strict; use warnings; use Time::HiRes 'time'; use Readonly; Readonly my $SIZE => 10_000_000; my $str; { # get us some data use String::Random 'random_regex'; srand 1234; $str = random_regex( "[ACTG]{$SIZE}" ); } { print "\nlet's test PDL!\n"; use PDL; my $t = time; my $p = PDL-> new_from_specification( byte, $SIZE ); ${ $p-> get_dataref } = $str; $p-> upd_data; my ( $lengths, $values ) = $p-> rle; my $cumu = $lengths-> cumusumover; my $C_lengths = $lengths * ( $values == ord 'C' ); my ( undef, $max, undef, $max_ind ) = $C_lengths-> minmaximum; report( $max, $cumu-> at( $max_ind - 1 ), time - $t ) } { print "\nlet's test pure Perl's re-engine!\n"; my $t = time; my $best = [ -1, -1 ]; while ( $str =~ /((C)\2+)/g ) { $best = [ length( $1 ), $-[ 1 ]] if length $1 > $best-> [ 0 ] } report( @$best, time - $t ) } sub report { printf "\tmax run of C's is %d bases long at %d\n\ttime consumed: +%f\n", @_ } __END__ let's test PDL! max run of C's is 11 bases long at 4367281 time consumed: 0.164513 let's test pure Perl's re-engine! max run of C's is 11 bases long at 4367281 time consumed: 0.361907

In reply to Re: substrings that consist of repeating characters by vr
in thread substrings that consist of repeating characters by Anonymous Monk

Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post; it's "PerlMonks-approved HTML":

  • Are you posting in the right place? Check out Where do I post X? to know for sure.
  • Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:
    <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>
  • Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
  • Want more info? How to link or How to display code and escape characters are good places to start.
Log In?

What's my password?
Create A New User
Domain Nodelet?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others examining the Monastery: (2)
As of 2023-09-25 22:13 GMT
Find Nodes?
    Voting Booth?

    No recent polls found