Camelia, the Perl 6 bug

IRC log for #bioperl, 2011-04-21

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All times shown according to UTC.

Time Nick Message
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12:42 dbolser can I use a DAS adaptor for a SF:Store in the same way as a mysql adaptor?
13:15 dbolser rbuels: about you're AGP BP module...
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13:15 dbolser how much work is it for it to inherit SeqFeature::StoreI?
13:16 dbolser It would be painfully useful for me right now if I could use an AGP object as a GBrowse adaptor
13:16 dbolser hello scottcain
13:16 scottcain good morning dbolser
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14:43 CIA-119 bioperl-run: Chris Fields master * r5d1d9d4 / Changes : a few last additions - http://bit.ly/fZ6j6e
15:31 rbuels dbolser: that AGP object shouldn't be a SeqFeature::StoreI.  but something could either inherit from or encapsulate *it* and glue it to SeqFeature::StoreI
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15:41 CIA-119 bioperl-run: Chris Fields master * raec2981 / Build.PL : passthrough Makefile is deprecated; add BEDTools dependency - http://bit.ly/fEDO36
15:41 CIA-119 bioperl-run: Chris Fields master * rfa29acb / (3 files in 2 dirs): hack in a workaround for version(), which conflicts with the -version parameter for BLAST+ - http://bit.ly/fOUGMF
15:50 CIA-119 bioperl-run: Chris Fields master * rfe5e5c0 / t/BEDTools.t : skip # off - http://bit.ly/hn9qjh
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15:55 dbolser rbuels: why is that better?
15:55 dbolser (me knows nothing)
15:56 dbolser rbuels: also, can you define a standard AGP -> GFF conversion and a) implement it in the AGP stuff you're doing and b) document it on the SO 'GFF best practice' page?
15:56 rbuels dbolser: so that people don't need all of bioperl to parse an AGP.
15:56 dbolser rbuels: right
15:56 dbolser that makes sense!
15:57 rbuels unless, like you, they want it.
15:57 dbolser sure
15:57 rbuels dbolser: you seen it in sheenams github?
15:57 rbuels dbolser: her pre-project was extracting that.
15:57 rbuels dbolser: https://github.com/sheenams/Bio-AGP
15:58 rbuels dbolser: it's almost ready to go to cpan
15:58 rbuels dbolser: that's gonna be her next task.
16:01 dbolser rbuels: awesome!
16:02 rbuels dbolser: feel free to submit pull requests.  it would be good for her to learn how they work.
16:02 dbolser ok
16:02 * dbolser begins stalking sheenams on github
16:02 rbuels (she's got a proposal in to get started on the bioperl breakup for gsoc)
16:03 rbuels (and it's a good proposal)
16:03 dbolser yeah, I caught some of that discussion in here
16:03 dbolser your master plan is coming together!
16:03 rbuels yep
16:03 dbolser slash and... slash
16:03 rbuels everything takes so *long* though
16:03 * rbuels sighs
16:04 dbolser rbuels: so long as each unit of functionality reduces the time taken to the next
16:05 rbuels dbolser: you talk to any PIs in your neighborhood about github for genomes?
16:05 rbuels really, somebody just needs to write a big grant and get money and do it
16:09 dbolser rbuels: ...
16:09 dbolser could that somebody be me?
16:09 rbuels could be.
16:09 dbolser I need a job that overlaps with my hobby
16:09 rbuels need more people though too
16:09 dbolser more than the current 70%
16:09 rbuels people with big powdered wigs
16:09 dbolser yeah...
16:10 rbuels to hem and haw and say how *interested* they are
16:10 dbolser I'm just of the opinion whatever I do EBI will poop on
16:10 rbuels maybe you need to work with EBI then
16:10 dbolser and unfortunately, I can't go to ebi
16:10 dbolser heh
16:15 * pyrimidine just got an image of Triumph the Insult Comic Dog
16:16 rbuels dbolser: you don't have to go to ebi, just find somebody in there that's interested in doing this
16:17 rbuels dbolser: and do a collaboration
16:17 rbuels or something.
16:20 dbolser rbuels: ic
16:20 dbolser just a quick question... If AGP object 'contains' several AGP components, how do you call the reverse relationship?
16:21 dbolser An AGP component 'belongs to' an AGP object?
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16:21 dbolser 'is part of'?
16:21 rbuels is a component of?
16:21 rbuels something like that
16:21 dbolser ok
17:31 CIA-119 bioperl-network: Chris Fields master * r9b0a1b5 / t/IO_psi10.t : get tests passing - http://bit.ly/dLThzi
17:31 pyrimidine :)
17:34 CIA-119 bioperl-network: Chris Fields master * r3cae3e6 / Build.PL : passthrough Makefile deprecated - http://bit.ly/h2MC66
17:35 CIA-119 bioperl-network: Chris Fields master * ra69d973 / Changes : small Changes update - http://bit.ly/gc5xsD
17:43 CIA-119 bioperl-network: Chris Fields master * r6caa4eb / Build.PL : add stub module_name - http://bit.ly/eYBp64
19:37 pyrimidine rbuels: around?
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