https://github.com/cjfields/bioperl6

reimplementation of BioPerl classes in Raku (e.g. the language formerly known as Perl6)
https://github.com/cjfields/bioperl6

bio bioinformatics bioperl perl6 raku rakudo

Last synced: 3 months ago
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reimplementation of BioPerl classes in Raku (e.g. the language formerly known as Perl6)

• Host: GitHub
• URL: https://github.com/cjfields/bioperl6
• Owner: cjfields
• License: artistic-2.0
• Created: 2009-02-11T21:04:55.000Z (almost 16 years ago)
• Default Branch: master
• Last Pushed: 2018-09-30T18:57:49.000Z (over 6 years ago)
• Last Synced: 2024-09-30T17:37:20.681Z (3 months ago)
• Topics: bio, bioinformatics, bioperl, perl6, raku, rakudo
• Language: Perl 6
• Homepage: http://bioperl.org
• Size: 582 KB
• Stars: 48
• Watchers: 9
• Forks: 13
• Open Issues: 6
• Metadata Files:
  • Readme: README.FIRST
  • License: LICENSE

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README

        
=BioPerl 6 (bioperl-experimental)=

The experimental classes in this directory are test implementations for Perl 6.

Most of these are similar to perl5-based BioPerl with simple Perl 6

translations. Hear thar be dragoons.

=Notes on Perl 6=

Perl 6 is a specification and thus can represent multiple implementations. We

recommend strictly following the Perl6 spec, defined in a series of synopses:

http://design.perl6.org/

Note that much of the specification is still in flux or is unfinished; much of

this is due to changes from experimenting with several preliminary Perl 6

implementations, such as Pugs or Rakudo (Perl 6 on Parrot), and parsing Perl 6

using Larry Wall's STD.pm grammar. 

Once the Perl 6 specification is considered complete, BioPerl 6 would then be

expected to run on any Perl 6 implementation passing the official Perl 6 test

suite. Until then, we will recommend the latest Parrot build from subversion

along with the latest Rakudo checkout (currently packaged with Parrot but soon

to be located in a separate repository). 

=Chris's Notes=

==Interfaces vs Classes==

In general, I am defining strict interfaces as roles and interface

implementations as classes. This is due to several interfaces actually defining

methods that are common to all implementations.

Defining interfaces as roles has a specific advantage, as roles can be mixed-in

per instance at runtime or class-wide at compile time:

# compile-time 

class Bio::PrimarySeq is Bio::Root::Root does Bio::RangeI {

   

}

# runtime mixin

my $seq = Bio.PrimarySeq.new();

my $seq does Bio::AnnotatableI;

==Class Methods==

Multiple dispatch. Named/positional/required/optional/slurpy/invocant

parameters. Type checking. Variable return contexts (scalar, list, hash, etc.).

==Named parameters==

Named parameters/arguments are now part of the Perl6 specification and can be

passed using comma notation or using Pairs:

my $seqobj = Bio::PrimarySeq.new(seq => $rawseq, description => $desc, :alphabet);

Note that this diverges from perl5-based BioPerl conventions, where named arguments are

prefixed with a dash ('-') character.

==Getter/Setters==

==Class Methods==

==Tests== 

None yet (soon to be added)