| Time |
Nick |
Message |
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| 12:29 |
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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... |
| 13:15 |
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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 |
| 13:38 |
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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 |
| 15:32 |
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| 15:34 |
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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 |
| 15:51 |
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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? |
| 16:21 |
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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? |
| 20:01 |
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