Camelia, the Perl 6 bug

IRC log for #bioruby, 2012-04-06

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All times shown according to UTC.

Time Nick Message
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07:18 Helius ciao
07:23 Helius csw:  hi, i'm reading just now
07:24 csw oh, fantastic
07:24 csw and hello!
07:31 Helius csw:  using berkeley db is just a matter of installing libraries like SQLite ?
07:32 csw Either that, or calling it directly
07:32 csw through the bdb gem, I suppose
07:35 Helius csw:  ok
07:37 Helius csw: http://genomewiki.ucsc.edu/index.php/​Whole_genome_alignment_howto#Example.2C_step_4:_Maffing http://hgdownload-test.cse.ucsc.​edu/goldenPath/hg19/multiz46way/
07:38 Helius csw:  from second link you can get real maf data
07:39 csw ah, thanks
07:40 csw I recall seeing some MAF data available from Galaxy, too, but I haven't gone back to find it again.
07:40 csw As far as SQLite or Berkeley DB goes, I'd envision using it in a similar way to this Biopython MAF code: https://github.com/polyatail/biopython​/blob/alignio-maf/Bio/AlignIO/MafIO.py
07:44 Helius csw:  ok, can you share berkeley db in the same way of sqlite ? just a matter of portability and reusing an index
07:46 csw I would definitely think so; I can't see why you couldn't.
07:46 Helius csw you could highlight that using berkeley or sqlite should be a matter of performances because API should be similar if not equal http://www.oracle.com/technetwork/products/be​rkeleydb/bdb-sqlite-comparison-wp-176431.pdf
07:47 csw definitely. And there is, for instance, Tokyo Cabinet which is in the same category and might be worth evaluating.
07:47 Helius so I think it's better if you highlight that in the proposal
07:48 csw that's very interesting about their API compatibility with SQLite.
07:48 Helius API and Tokyo Cabinet
07:49 Helius csw:  yep ! you see how it could be important ?
07:50 Helius compatibility is very important and I think that supporting bx-python index could be important too, a developer could process a maf with python and another one could reuse it's index from ruby
07:51 csw indeed. Also, that document makes it sound like Berkeley DB might be a bit more tricky to move around than SQLite, since it keeps several files per database.
07:54 Helius yesterday I read that berkeley is portable in the way, there are no problems with big/litter endian / architectures.  I would only spend more time on bx-python index than extreme performances tuning with foreign languages. btw I agree with the plan.
07:54 Helius coffe time :-)
07:54 csw and bed time for me, I think :)
07:54 Helius lol
07:55 csw it's good to not have to worry about endianness issues, although it's been a while since I've used a big-endian machine.
07:56 Helius mee to
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