Re: perl6 vs ruby

[Fields, Christopher J]

A few people had started a port of some BioPerl code to Perl6 a while ago; I 
tested this recently and it still passed tests.

https://github.com/cjfields/bioperl6

It should be renamed to bioraku!

Chris

Sent from my iPhone

On Mar 3, 2020, at 11:41 AM, Parrot Raiser <1parr...@gmail.com> wrote:


we use ruby for Biological data analysis. I wish perl6 should have got that 
capability.

Would you like to give us a sample problem,, to see if someone can
show a potential solution?

Re: A practical benchmark shows speed challenges for Perl 6

[Fields, Christopher J]

On Mar 31, 2016, at 8:56 AM, Tom Browder 
> wrote:

On Thursday, March 31, 2016, Elizabeth Mattijsen 
> wrote:
> On 31 Mar 2016, at 14:12, Tom Browder > 
> wrote:
> Liz, it's a simple reader of a text file.  The only line processing is a 
> print of the number of characters of each line.  I guess I should eliminate 
> that but I assumed that was neglible since all the reader scripts do the same.

I wonder.  I wouldn’t be surprised if not printing number of chars would make a 
significant difference.

I'll try turning any line processing off, but note the Perl 5 reader does the 
same thing.

Best,

-Tom

Just to note, I have also seen dramatic differences in IO between Perl 5 and 
Perl 6, simply iterating through large files (in this case DNA sequence data) 
by line w/ no processing.

Chris

Re: books on p6?

[Fields, Christopher J]

Of course! the base URL has posts :P

http://www.learningperl6.com/

Knew I saw it somewhere...

Chris

On Mar 11, 2016, at 8:28 AM, Fields, Christopher J 
<cjfie...@illinois.edu<mailto:cjfie...@illinois.edu>> wrote:

The below link indicates an update in Dec. 2015.  I also recall seeing 
something after the Christmas release, maybe from brian d foy, which indicated 
this is still being worked on.

http://www.learningperl6.com/book/

Chris

On Mar 11, 2016, at 7:56 AM, Will Coleda 
<w...@coleda.com<mailto:w...@coleda.com>> wrote:

ISTR that link has been around for ages. I don't think they're
actually working on that book anymore.

On Thu, Mar 10, 2016 at 5:06 PM, Steve Mynott 
<steve.myn...@gmail.com<mailto:steve.myn...@gmail.com>> wrote:
See http://www.learningperl6.com/about/

Although this is still vapourware and the current best resources are
linked from the perl6.org<http://perl6.org> web pages.

S

On 10 March 2016 at 15:07, Brock Wilcox 
<awwa...@thelackthereof.org<mailto:awwa...@thelackthereof.org>> wrote:
Yes, that is out of date. I don't know of any existing books or public
efforts to write ones.

We welcome contributions to docs.perl6.org<http://docs.perl6.org>, including 
tutorials,
walk-throughs, etc (beyond just references). That resource is getting
better, but slowly :)

--Brock


On Thu, Mar 10, 2016 at 3:59 AM, Luca Ferrari 
<fluca1...@infinito.it<mailto:fluca1...@infinito.it>> wrote:

Hi all,
anybody knows of ongoing efforts for Perl 6 related books?
I suspect O'reilly title
<http://shop.oreilly.com/product/9780596007379.do> is pretty much out
of date, or am I wrong?

Thanks,
Luca



--
4096R/EA75174B Steve Mynott 
<steve.myn...@gmail.com<mailto:steve.myn...@gmail.com>>



--
Will "Coke" Coleda

Re: books on p6?

[Fields, Christopher J]

The below link indicates an update in Dec. 2015.  I also recall seeing 
something after the Christmas release, maybe from brian d foy, which indicated 
this is still being worked on.

http://www.learningperl6.com/book/

Chris

> On Mar 11, 2016, at 7:56 AM, Will Coleda  wrote:
> 
> ISTR that link has been around for ages. I don't think they're
> actually working on that book anymore.
> 
>> On Thu, Mar 10, 2016 at 5:06 PM, Steve Mynott  wrote:
>> See http://www.learningperl6.com/about/
>> 
>> Although this is still vapourware and the current best resources are
>> linked from the perl6.org web pages.
>> 
>> S
>> 
>>> On 10 March 2016 at 15:07, Brock Wilcox  wrote:
>>> Yes, that is out of date. I don't know of any existing books or public
>>> efforts to write ones.
>>> 
>>> We welcome contributions to docs.perl6.org, including tutorials,
>>> walk-throughs, etc (beyond just references). That resource is getting
>>> better, but slowly :)
>>> 
>>> --Brock
>>> 
>>> 
 On Thu, Mar 10, 2016 at 3:59 AM, Luca Ferrari  
 wrote:
 
 Hi all,
 anybody knows of ongoing efforts for Perl 6 related books?
 I suspect O'reilly title
  is pretty much out
 of date, or am I wrong?
 
 Thanks,
 Luca
>> 
>> 
>> 
>> --
>> 4096R/EA75174B Steve Mynott 
> 
> 
> 
> -- 
> Will "Coke" Coleda

Re: Is there an equivalent env var to PERL5LIB for Perl 6 module locations?

[Fields, Christopher J]

On Mar 31, 2015, at 6:28 AM, Paul Cochrane p...@liekut.de wrote:
 
 On Tue, Mar 31, 2015 at 05:40:44AM -0500, Tom Browder wrote:
 On Mon, Mar 30, 2015 at 7:35 PM, Rob Hoelz r...@hoelz.ro wrote:
 Yup, PERL6LIB. =)
 
 And how did you find out about it, i.e., where is it documented?
 
 http://doc.perl6.org/language/5to6#Environment_variables
 
 to be honest I cheated and have written the docs just today.  :-)
 
 A `git grep LIB` in the spec sources turned up the text on environment
 variables in S19, so that'd be one place to check as well.  In general, if a
 search like that doesn't seem to turn up much, a `git grep` in the Rakudo
 sources also turns up quite a bit of info.
 
 Cheers,
 
 Paul

Funny, I had been using PERL6LIB for a number of years now and had assumed it 
was already documented (I recall it’s use popping up on IRC a number of years 
ago, which is where I picked it up).

chris

Grammars and biological data formats

[Fields, Christopher J]

(accidentally sent to perl6-lang, apologies for cross-posting but this seems 
more appropriate)

I have a fairly simple question regarding the feasibility of using grammars 
with commonly used biological data formats.  

My main question: if I wanted to parse() or subparse() vary large files (not 
unheard of to have FASTA/FASTQ or other similar data files exceed 100’s of GB) 
would a grammar be the best solution?  For instance, based on what I am reading 
the semantics appear to be greedy; for instance:

   Grammar.parsefile($file)

appears to be a convenient shorthand for:

   Grammar.parse($file.slurp)

since Grammar.parse() works on a Str, not a IO::Handle or Buf.  Or am I 
misunderstanding how this could be accomplished?

(just to point out, I know I can subparse() as well but that also appears to 
act on a string…)

As an example, I have a simple grammar for parsing FASTA, which a (deceptively) 
simple format for storing sequence data:

   http://en.wikipedia.org/wiki/FASTA_format

I have a simple grammar here:

   https://github.com/cjfields/bioperl6/blob/master/lib/Bio/Grammar/Fasta.pm6

and tests here:

   https://github.com/cjfields/bioperl6/blob/master/t/Grammar/fasta.t

Tests pass with the latest Rakudo just fine.

chris

Re: Grammars and biological data formats

[Fields, Christopher J]

 On Aug 9, 2014, at 5:25 PM, t...@wakelift.de t...@wakelift.de wrote:
 
 
 On 08/10/2014 12:21 AM, t...@wakelift.de wrote:
 Something that does surprise me is that your tests seem to imply that :p
 for subparse doesn't work. I'll look into that, because I believe it
 ought to be implemented already. Perhaps not properly hooked up, though.
 
 On #perl6 I got corrected quite quickly: subparse is anchored to the
 start and end of the target string, so :pos doesn't make sense. In this
 case, you want just .parse

I mainly tested subparse() to see if it would find the second FASTA record 
(which works if using :p and not :pos).

Sorry, I should have updated that, but subparse() with :p works fine; the spec 
mentions :pos though (I plan on submitting a pull request on that).

 Another thing is that if lines() does keep all data around, it should be
 considered a bug, as we should be able to infer that we don't keep the
 list itself around and thus won't be able to refer to its previous
 values later on. Thus, we should free the memory for the earlier lines
 in the target string after the loop is done with them.
 
 I have not yet tested, if this is the case, though.
 
 Hope that clears up a bit of potential confusion before it can arise
  - Timo

I can try that out.

Chris