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Liz

  • Website: www.liz.nl
  • About: I must blog about Perl
  • Commented on Cleaning up the IDs in a FASTA file
    split() currently does not create a lazy list. If the grammar engine is used to split, it creates all Match objects prior to returning and starting to hand them back. If it is not, it is using the internal nqp::split...
  • Commented on FASTQ to FASTQ with Perl 6
    Cool! FWIW, you don't have to name variables that you don't use (but that you do want to "consume") in the for loop. So: for $fastq.IO.lines -> $header, $seq, $, $ { ... } is also perfectly valid....
  • Commented on Cleaning up the IDs in a FASTA file
    FWIW, I would write the inner for loop as: $tmpfh.say( .starts-with(">") ?? ">" ~ .split('|')[1] !! $_ ) for $file.IO.lines; :-)...
  • Commented on Why I try to avoid Perl's punctuation variables
    FWIW, if you don't want to create another lexical, you can still use @{[ ]} with a join inside there, no? my $query = <<"END_SQL"; SELECT foo, bar, baz FROM SomeTable WHERE id IN @{[ join ', ' => ('?')...
  • Commented on Concurrency Weirdness
    Ah, yes, arrays are not thread safe if you have on thread adding and another thread removing. Please use Channels for that (the P6 equivalent to P5's Thread::Queue). Locks should probably never be used in any user code....
  • Commented on Concurrency Weirdness
    I first tried to minimize the functionality as I understand it: sub MAIN($lines) { .say for $*IN.lines.tail($lines); } This works fine. Then I tried mixing in the named pipe. sub MAIN( $lines, $pipefile ){ my $p = run << mkfifo...
  • Commented on Further Perl 6 Adventures
    $ 6 'sub a($a,$b) { }; &a.signature.perl.say' :($a, $b) $ 6 'my $b = -> $a,$b { }; $b.signature.perl.say' :($a, $b) Signatures are an object, just like any other thing in Perl 6. Any Callable has it, and it...
  • Commented on Async Aborts and P6SGI
    Thank you for this bug report. Not being a MoarVM / libuv person much myself, I won't act on it in the near future. But I'm pretty sure some other people will soon!...
  • Commented on Christmas Came, Bah Humbug
    As I stated in my London Perl Workshop Keynote, this is just the End of the Beginning. I agree that for Perl 6 to take off, there needs to be a business case for it. In 2016 we will see...
  • Posted Christmas Is Here! to Liz

    Check out the final Perl 6 Advent post of 2015.

    Also check out Jonathan Worthington's thoughts on the 6.c release o…

  • Commented on Fluent interfaces in Perl 6
    Cool! One remark: you don't need a closure for showing an attribute in a string, so: qq/Name: $.name/ will just do fine!...
  • Commented on Is Perl still a useful, viable language?
    I agree that Perl is the future. However, I think that if you think Perl's future depends on Larry's decision on what to name the next version of Perl, you are both demeaning to the fine folks that keep working...
  • Commented on Mystery Line in Proc Input in Perl 6
    Looking into it, it appears there is a different logic in setting EOF between getting a handle from a file, or from a process. The latter appears to be setting EOF too late, hence the extra empty line. Determining cause...
  • Commented on Refactoring Very Old Perl 5 in Perl 6
    Martin Hradil: re .index returning 0 but True? Alas, it didn't make it past TimToady's vetting in the long run :-( I removed that feature yesterday again, Long story: the feature was implemented using a subclass of Int, basically: class...
  • Commented on Refactoring Very Old Perl 5 in Perl 6
    Great post! Some comments: 1. You're using .trim the wrong way: .trim does *not* modify $_. It should probably warn in that case, actually. 2. You don't need .trim at all, as .words ignores any whitespace at the begin or...
  • Commented on Method Privacy in Perl
    Perhaps a source of enlightenment: http://perlcabal.org/syn/S12.html#Submethods...
  • Commented on Rakudo and NQP Internals Workshop (14/15 Sep)
    Down to 2...
  • Commented on Rakudo and NQP Internals Workshop (14/15 Sep)
    Actually, down to 3 now!...
  • Posted Rakudo and NQP Internals Workshop (14/15 Sep) to Liz

    Perl6 is at a turning point. Now running on 2 virtual machines (Parrot and JVM), with 2 more coming available in the next months (Javascript and MoarVM), with abstract concurrency on the JVM now and full Perl 5 interop at the horizon in MoarVM.

    To make it easier for past, current and futu…

  • Commented on YAPC::Europe 2013 in Kiev, week minus 19
    Some people in the Ukraine may not like "Back in the USSR" as the background music. Then again, it *is* April 1st :-)...
  • Commented on Why I'm considering dropping Perlmonks
    I left PerlMonks a long time ago already but for a technical reason: it is just too damn slow. I was impressed by Schwern's YAPC keynote. The comic strip is just bad and in bad taste. As far as I'm...
  • Posted Perl Reunification Summit to Liz

    As some of you may know, my partner Wendy van Dijk and me organized a Perl Reunification Summit on the Friday and Saturday before the YAPC::Europe. Organizing this started in May already, when I tried to contact as many people face to face to discuss this, before finalizing the plan. When the…

  • Posted First Post to Liz

    So, why don't you write a blog? A question I have been asked many a time in the past years.

    I guess I mainly felt that I didn't have to tell the world much. And I was busy with $work.

    Then you stop $work and start with $sabbatical. And start acting on the strange ideas that you …

  • Commented on So, Kiev 2013
    Please make sure that he gets a visa. Otherwise, I understand, he will not be let into the Ukraine (as Australia is one of the few countries of which its citizens need a visa to travel to the Ukraine)....
  • Commented on post-yapc
    Steven: Perl 5 momentum is much on everybody’s mind. The last thing I want is to do, is to take people away from Perl 5 development. What I do want to achieve, is a long term environment in which Perl...
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  • Steve Nolte commented on Why I try to avoid Perl's punctuation variables

    I applaud this article and others like it. At $work we are constantly fighting bugs in code that is "too clever" and not explicit. Also fascinating to see what may seem obvious to some (e.g. the Babycart operator) but quite confusing to newbies.

  • Pawel bbkr Pabian commented on Cleaning up the IDs in a FASTA file

    Does split produce lazy list in Perl 6?
    split('|')[1]
    Will it read all fields in memory or just stop after finding second?


    BTW: How did you start your career in bioinformatics? Was your primary education biology/genetics and you used Perl as a tool to solve your tasks, or was it the other way - you were a bored programmer that thought one day "it would be cool to sequence and save my hamster to hard drive"?
    What is the bio knowledge threshold required to start work in bioinformatics company?

  • kyclark commented on Cleaning up the IDs in a FASTA file

    "starts-with" is a great thing to show my beginner students! I keep forgetting about that, but it's a nice borrow from Python. Thanks!

  • kyclark commented on Cleaning up the IDs in a FASTA file

    Pawel, I accidentally stumbled into bioinformatics. I was a Perl hacker who got hired by Lincoln Stein back in 2001 to work at Cold Spring Harbor Lab. It was immediately fascinating and horribly intimidating. I have never felt even a little bit competent as a biologist, but I keep trying to learn as much as possible. After working for CSHL (on the Gramene.org project), I moved to the Univ. of Arizona where I work for Dr. Bonnie Hurwitz in a field called "metagenomics." I'm still in way over my head, but she puts up with me because I can hack together pipelines. So, just keep learning,…

  • kyclark commented on FASTQ to FASTQ with Perl 6

    Wow, thanks, Liz! That is really cool.

    Also, the title should have been "FASTQ to FASTA." Darn.

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