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bioperl6

reimplementation of BioPerl classes in Perl6

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Statistics on bioperl6

Number of watchers on Github 44
Number of open issues 1
Average time to close an issue 6 months
Main language Perl6
Average time to merge a PR 21 days
Open pull requests 0+
Closed pull requests 0+
Last commit almost 2 years ago
Repo Created over 10 years ago
Repo Last Updated over 1 year ago
Size 597 KB
Homepage http://bioperl.org
Organization / Authorcjfields
Contributors7
Page Updated
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Build Status

BioPerl 6

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. We intend on porting functionality when needed, but also addressing many of the problems faced with the perl5 BioPerl version, namely class/interface structure, overly complex class hierarchy, etc.

So, keep in mind that nothing is set in stone yet and things may change under your feet. Hic sunt dracones.

Also, just a note: this repository may eventually be moved under the BioPerl umbrella. If so, I'll leave stub repo here pointing to the correct location.

Participation

If you have an itch to scratch and want to try it out, fork the code and hack away. Even better, I can add you as a developer! Drop me a note, I'm more than happy to have help. The more the better!

Targeting

Currently, I target Rakudo Perl 6 (specifically using the MoarVM backend) off the nom branch. We may switch at some point to a targeted Rakudo Star version for more stability, but since the latest branch code has seen dramatic improvements (as of Aug. 2014) we aim to stay consistent with that.

Note, as of Dec. 25, 2015, Rakudo is now targeting the newly-released Perl 6 official specification (6.c), therefore syntax is expected to have stabilized and focus will be fixing bugs, improving performance, and working out corners of the specification that need further clarification.

Implemented

  • Bio::PrimarySeq - this includes required basic modules for transcription and translation.
  • Bio::Range - simple biological range operations (don't confuse this with the Perl 6 Range class)
  • Bio::Root - original base class for BioPerl, though this may be removed in favor of using Perl 6 standard exception handling (which is leagues better than p5)

Testing

Basically, one can do this:

prove -e 'perl6' -r t

which will run all tests. This will certainly fail at this stage! Most current tests are ports from the original BioPerl distribution, and the current code is in various stages of updating. We anticipate this changing more over the next year.

To run a single test:

prove -e 'perl6' t/Root.t

Notes

Perl 6 is a specification and thus can represent multiple implementations. More in the Perl 6 synopses.

Related

  • Matt Oates has some nice Perl6 bioinformatics code implemented in the BioInfo project that demonstrates some of the power of Perl6, including slangs and concurrency.
bioperl6 list of languages used
  • Perl 6
Other projects in Perl6