Camelia, the Perl 6 bug

IRC log for #bioperl, 2012-04-02

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All times shown according to UTC.

Time Nick Message
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17:01 brrt pyrimidne, do you have time?
17:06 pyrimidine brrt: a bit
17:06 brrt :-)
17:07 brrt I was just writing a response to your (and leon's) e-mail
17:07 brrt I was hoping for your advice w/ regards to the scope of the project
17:08 pyrimidine sure
17:08 brrt personally, i was thinking to limit it (mostly) to IO
17:09 brrt that is, file format import / export, database connections and such
17:09 pyrimidine I think if you keep it simple on IO w/ perl 6 it might be better
17:09 pyrimidine I think that's still a flaky area in the spec
17:09 pyrimidine but maybe it's settling out (I believe moritz or masak were on that)
17:10 pyrimidine DB would be very nice
17:11 pyrimidine on file formats, something simple to start with would be FASTA, but there is an example of that in the github repo
17:12 brrt repo of bioperl6?
17:12 pyrimidine yup
17:12 pyrimidine https://github.com/cjfields/bioperl6
17:12 brrt i see
17:12 brrt looks simple enough
17:13 pyrimidine (that may become part of the official bioperl org at some point)
17:13 pyrimidine Philip Mabon (takadonet on #perl6) contributed the FASTA grammar: https://github.com/cjfields/bioperl6/​blob/master/lib/Bio/Grammar/Fasta.pm
17:13 pyrimidine but I don't think it's current to spec
17:14 pyrimidine very simple, thoughm should be easy enough to fix it
17:14 pyrimidine *though
17:14 brrt i could try to fix it to run in rakudo
17:14 brrt i run linux so rakudo is the most obvious target for me
17:14 pyrimidine niecza runs fine with mono
17:15 pyrimidine I have tested it on my ubuntu box, but I know some devs have, let's called it 'issues', with using mono
17:15 brrt hmm, as in, dislike?
17:16 pyrimidine problems with licensing due to M$
17:16 pyrimidine chromatic, for one, won't touch it from what I understand
17:17 brrt i see...
17:17 brrt for me personally i'd like to develop in rakudo first, niecza second
17:18 pyrimidine re: mono and patents: http://en.wikipedia.org/wiki/Mon​o_(software)#Mono_and_Microsoft.27s_patents
17:19 pyrimidine re:rakudo first, that's probably a good idea, but I personally don't have a problem with mono
17:19 pyrimidine I also see that you have checked out biome, that's also a possibility
17:20 pyrimidine I have worked more on that than bioperl6 by far
17:20 pyrimidine but it's still in a sub-optimal state
17:20 pyrimidine (but hey, lots of stuff works)
17:21 brrt that's true
17:21 brrt is it feasible to run oldschool bioperl modules in a moose-enviroment, or would that mean loading two different systems alongside each other?
17:21 brrt anyway, perl6 is just a personal preference
17:22 pyrimidine you can run the two somewhat together, but I am taking the route of a reimplementation with the end purpose of simplifying things
17:23 pyrimidine in other words, they are both perl5 but they don't have the same class architecture (primarily b/c we get rid of interfaces for roles, etc)
17:25 brrt yes, i see
17:25 brrt i'm actually not very familiar with moose
17:26 pyrimidine brrt: it's up to you
17:27 brrt :-) that's true
17:27 pyrimidine personally, if I had time I would focus more on the perl 6 side
17:27 pyrimidine for the same reasons you mention (getting users involved with perl 6)
17:28 pyrimidine but I also have to get work done, and perl 6's state is still in 'early adopter' mode
17:28 pyrimidine even TimToady says so
17:29 brrt on the other hand, if no one uses it, it will stay in early adopter mode
17:29 pyrimidine right
17:32 brrt anyway, I think getting the FASTA grammar to work is a good challenge for tonight :-)
17:32 pyrimidine sure, go for it
17:32 brrt btw, and this is really a noob question
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17:32 brrt ... which are the 'important' databases for bioperl in practice?
17:33 pyrimidine RDBMS, or schema?
17:33 brrt ehm, I don't know, honestly :-)
17:34 pyrimidine RDBMS = MySQL, Pg for the majority of applications (SQLite for lightweight stuff)
17:34 pyrimidine schema = lots :)
17:35 brrt hmm... i can't possibly code to all schemas
17:35 pyrimidine I wouldn't worry as much about the schema
17:35 pyrimidine getting basic DB connectivity would work wonders
17:36 pyrimidine e.g. opens up a lot of possibilities
17:36 brrt that isn't there right now?
17:37 pyrimidine it's there, but I think it's somewhat limited
17:38 pyrimidine might be worth asking around on #perl6
17:38 brrt i will
17:38 brrt thanks a lot :-)
17:38 pyrimidine np
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